1
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Rocha ME, Mangiavacchi N, Marques M, Teixeira L. Succession from acetoclastic to hydrogenotrophic microbial community during sewage sludge anaerobic digestion for bioenergy production. Biotechnol Lett 2024:10.1007/s10529-024-03528-6. [PMID: 39261355 DOI: 10.1007/s10529-024-03528-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 08/06/2024] [Accepted: 08/28/2024] [Indexed: 09/13/2024]
Abstract
To assess microbial dynamics during anaerobic digestion (AD) of sewage sludge (SWS) from a municipal Wastewater Treatment Plant (WWTP), a Biochemical Methane Potential (BMP) assay at 37 °C under mono-digestion conditions was conducted. Utilizing the Illumina MiSeq platform, 16S ribosomal RNA (rRNA) gene sequencing unveiled a core bacterial community in the solid material, showcasing notable variations in profiles. The research investigates changes in microbial communities and metabolic pathways to understand their impact on the efficiency of the digestion process. Prior to AD, the relative abundance in SWS was as follows: Proteobacteria > Bacteroidota > Actinobacteriota. Post-AD, the relative abundance shifted to Firmicutes > Synergistota > Proteobacteria, with Sporanaerobacter and Clostridium emerging as dominant genera. Notably, the methanogenic community underwent a metabolic pathway shift from acetoclastic to hydrogenotrophic in the lab-scale reactors. At the genus level, Methanosaeta, Methanolinea, and Methanofastidiosum predominated initially, while post-AD, Methanobacterium, Methanosaeta, and Methanospirillum took precedence. This metabolic transition may be linked to the increased abundance of Firmicutes, particularly Clostridia, which harbor acetate-oxidizing bacteria facilitating the conversion of acetate to hydrogen.
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Affiliation(s)
- Mariana Erthal Rocha
- Department of Mechanical Engineering, Rio de Janeiro State University, Rio de Janeiro, Brazil.
- Department of Sanitary and Environmental Engineering, Rio de Janeiro State University, Rio de Janeiro, Brazil.
| | - Norberto Mangiavacchi
- Department of Mechanical Engineering, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Marcia Marques
- Department of Sanitary and Environmental Engineering, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Lia Teixeira
- Department of Sanitary and Environmental Engineering, Rio de Janeiro State University, Rio de Janeiro, Brazil
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2
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Yang T, Chavez MS, Niman CM, Xu S, El-Naggar MY. Long-distance electron transport in multicellular freshwater cable bacteria. eLife 2024; 12:RP91097. [PMID: 39207443 PMCID: PMC11361709 DOI: 10.7554/elife.91097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
Filamentous multicellular cable bacteria perform centimeter-scale electron transport in a process that couples oxidation of an electron donor (sulfide) in deeper sediment to the reduction of an electron acceptor (oxygen or nitrate) near the surface. While this electric metabolism is prevalent in both marine and freshwater sediments, detailed electronic measurements of the conductivity previously focused on the marine cable bacteria (Candidatus Electrothrix), rather than freshwater cable bacteria, which form a separate genus (Candidatus Electronema) and contribute essential geochemical roles in freshwater sediments. Here, we characterize the electron transport characteristics of Ca. Electronema cable bacteria from Southern California freshwater sediments. Current-voltage measurements of intact cable filaments bridging interdigitated electrodes confirmed their persistent conductivity under a controlled atmosphere and the variable sensitivity of this conduction to air exposure. Electrostatic and conductive atomic force microscopies mapped out the characteristics of the cell envelope's nanofiber network, implicating it as the conductive pathway in a manner consistent with previous findings in marine cable bacteria. Four-probe measurements of microelectrodes addressing intact cables demonstrated nanoampere currents up to 200 μm lengths at modest driving voltages, allowing us to quantify the nanofiber conductivity at 0.1 S/cm for freshwater cable bacteria filaments under our measurement conditions. Such a high conductivity can support the remarkable sulfide-to-oxygen electrical currents mediated by cable bacteria in sediments. These measurements expand the knowledgebase of long-distance electron transport to the freshwater niche while shedding light on the underlying conductive network of cable bacteria.
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Affiliation(s)
- Tingting Yang
- Department of Physics and Astronomy, University of Southern CaliforniaLos AngelesUnited States
| | - Marko S Chavez
- Department of Physics and Astronomy, University of Southern CaliforniaLos AngelesUnited States
| | - Christina M Niman
- Department of Physics and Astronomy, University of Southern CaliforniaLos AngelesUnited States
| | - Shuai Xu
- Department of Physics and Astronomy, University of Southern CaliforniaLos AngelesUnited States
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern CaliforniaLos AngelesUnited States
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern CaliforniaLos AngelesUnited States
- Department of Chemistry, University of Southern CaliforniaLos AngelesUnited States
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3
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Wu Z, Sun J, Xu L, Zhou H, Cheng H, Chen Z, Wang Y, Yang J. Depth significantly affects plastisphere microbial evenness, assembly and co-occurrence pattern but not richness and composition. JOURNAL OF HAZARDOUS MATERIALS 2024; 463:132921. [PMID: 37944228 DOI: 10.1016/j.jhazmat.2023.132921] [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: 09/02/2023] [Revised: 10/12/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023]
Abstract
Microplastics have become one of the hot concerns of global marine pollution. In recent years, diversity and abiotic influence factors of plastisphere microbial communities were well documented, but our knowledge of their assembly mechanisms and co-occurrence patterns remains unclear, especially the effects of depth on them. Here, we collected microorganisms on microplastics to investigate how ocean depth affects on microbial diversity, community composition, assembly processes and co-occurrence patterns. Our results indicated that there were similar microbial richness and community compositions but microbial evenness and unique microbes were obviously different in different ocean layers. Our findings also demonstrated that deterministic processes played dominant roles in the assembly of the mesopelagic plastisphere microbial communities, while the bathypelagic microbial community assembly was mainly shaped by stochastic processes. In addition, the co-occurrence networks suggested that the relationships between microorganisms in the mesopelagic layer were more complex and stable than those in the bathypelagic layer. Simultaneously, we also found that Proteobacteria and Actinobacteriota were the most abundant keystones which played important roles in microbial co-occurrence networks at both layers. This study enhanced our understanding of microbial diversity, assembly mechanism, and co-occurrence pattern on plastisphere surfaces, and provided useful insights into microorganisms capable of degrading plastics and microbial remediation.
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Affiliation(s)
- Zhiqiang Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China
| | - Jianxing Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China
| | - Liting Xu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha 410083, Hunan, PR China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha 410083, Hunan, PR China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha 410083, Hunan, PR China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha 410083, Hunan, PR China.
| | - Jichao Yang
- College of Marine Science and Engineering, Shandong University of Science and Technology, Qingdao 266590, Shandong, PR China.
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4
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Skoog EJ, Bosak T. Predicted metabolic roles and stress responses provide insights into candidate phyla Hydrogenedentota and Sumerlaeota as members of the rare biosphere in biofilms from various environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13228. [PMID: 38192240 PMCID: PMC10866078 DOI: 10.1111/1758-2229.13228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/11/2023] [Indexed: 01/10/2024]
Abstract
Pustular mats from Shark Bay, Western Australia, host complex microbial communities bound within an organic matrix. These mats harbour many poorly characterized organisms with low relative abundances (<1%), such as candidate phyla Hydrogenedentota and Sumerlaeota. Here, we aim to constrain the metabolism and physiology of these candidate phyla by analyzing two representative metagenome-assembled genomes (MAGs) from a pustular mat. Metabolic reconstructions of these MAGs suggest facultatively anaerobic, chemoorganotrophic lifestyles of both organisms and predict that both MAGs can metabolize a diversity of carbohydrate substrates. Ca. Sumerlaeota possesses genes involved in degrading chitin, cellulose and other polysaccharides, while Ca. Hydrogenedentota can metabolize cellulose derivatives in addition to glycerol, fatty acids and phosphonates. Both Ca. phyla can respond to nitrosative stress and participate in nitrogen metabolism. Metabolic comparisons of MAGs from Shark Bay and those from various polyextreme environments (i.e., hot springs, hydrothermal vents, subsurface waters, anaerobic digesters, etc.) reveal similar metabolic capabilities and adaptations to hypersalinity, oxidative stress, antibiotics, UV radiation, nitrosative stress, heavy metal toxicity and life in surface-attached communities. These adaptations and capabilities may account for the widespread nature of these organisms and their contributions to biofilm communities in a range of extreme surface and subsurface environments.
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Affiliation(s)
- Emilie J. Skoog
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Integrative Oceanography DivisionScripps Institution of Oceanography, UC San DiegoLa JollaCaliforniaUSA
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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Sun K, Yu M, Zhu XY, Xue CX, Zhang Y, Chen X, Yao P, Chen L, Fu L, Yang Z, Zhang XH. Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole. Microbiol Spectr 2023; 11:e0114923. [PMID: 37623326 PMCID: PMC10580873 DOI: 10.1128/spectrum.01149-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/13/2023] [Indexed: 08/26/2023] Open
Abstract
The Sansha Yongle Blue Hole (SYBH), the deepest blue hole in the world, is an excellent habitat for revealing biogeochemical cycles in the anaerobic environment. However, how sulfur cycling is mediated by microorganisms in the SYBH hasn't been fully understood. In this study, the water layers of the SYBH were divided into oxic zone, hypoxic zone, anoxic zone I and II, and microbial-mediated sulfur cycling in the SYBH was comprehensively interpreted. The 16S rRNA genes/transcripts analyses showed that the microbial community structures associated with the sulfur cycling in each zone had distinctive features. Sulfur-oxidizing bacteria were mostly constituted by Gammaproteobacteria, Alphaproteobacteria, Campylobacterota, and Chlorobia above the anoxic zone I and sulfate-reducing bacteria were dominated by Desulfobacterota in anoxic zones. Metagenomic analyses showed that the sulfide-oxidation-related gene sqr and genes encoding the Sox system were mainly distributed in the anoxic zone I, while genes related to dissimilatory sulfate reduction and sulfur intermediate metabolite reduction were mainly distributed in the anoxic zone II, indicating different sulfur metabolic processes between these two zones. Moreover, sulfur-metabolism-related genes were identified in 81 metagenome-assembled genomes (MAGs), indicating a high diversity of microbial communities involved in sulfur cycling. Among them, three MAGs from the candidate phyla JdFR-76 and AABM5-125-24 with genes related to dissimilatory sulfate reduction exhibited distinctive metabolic features. Our results showed unique and novel microbial populations in the SYBH sulfur cycle correlated to the sharp redox gradients, revealing complex biogeochemical processes in this extreme environment. IMPORTANCE Oxygen-deficient regions in the global ocean are expanding rapidly and affect the growth, reproduction and ecological processes of marine organisms. The anaerobic water body of about 150 m in the Sansha Yongle Blue Hole (SYBH) provided a suitable environment to study the specific microbial metabolism in anaerobic seawater. Here, we found that the vertical distributions of the total and active communities of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) were different in each water layer of the SYBH according to the dissolved oxygen content. Genes related to sulfur metabolism also showed distinct stratification characteristics. Furthermore, we have obtained diverse metagenome-assembled genomes, some of which exhibit special sulfur metabolic characteristics, especially candidate phyla JdFR-76 and AABM5-125-24 were identified as potential novel SRB. The results of this study will promote further understanding of the sulfur cycle in extreme environments, as well as the environmental adaptability of microorganisms in blue holes.
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Affiliation(s)
- Kai Sun
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Min Yu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao-Yu Zhu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chun-Xu Xue
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunhui Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xing Chen
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Lin Chen
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Liang Fu
- Sansha Track Ocean Coral Reef Conservation Research Institute, Sansha, China
| | - Zuosheng Yang
- College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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6
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Nagarajan V, Tsai HC, Chen JS, Koner S, Kumar RS, Chao HC, Hsu BM. Systematic assessment of mineral distribution and diversity of microbial communities and its interactions in the Taiwan subduction zone of mud volcanoes. ENVIRONMENTAL RESEARCH 2023; 216:114536. [PMID: 36228688 DOI: 10.1016/j.envres.2022.114536] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/11/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Mud volcanoes are the most dynamic and unstable sedimentary structures in the areas of tectonic compression like the subduction zones. In this study, we comprehensively analyzed the distribution of minerals as well as diversity, abundance and metabolic potential of the microbial communities of major mud volcanic groups across Taiwan namely Chu-kou Fault (CKF), Gu-ting-keng Anticline (GTKA), Chi-shan Fault (CSF), and Longitudinal Valley Fault (LVF). The mud volcano fluids recorded relatively higher Na and Cl contents than the other elements, particularly in the CKF and GTKA groups. The highest microbial diversity and richness were observed in the CSF group, followed by the GTKA group, whereas the lowest microbial diversity was observed in the CKF and LVF groups. Proteobacteria were common in all the sampling sites, except WST-7 and WST-H (Wu-Shan-Ting) of the CSF group, which were abundant in Chloroflexi. The halophilic genus Alterococcus was abundant in the Na-and Cl-rich CL-A sites of the CKF group. Sulfurovum was dominant in the CLHS (Chung-Lun hot spring) site of the CKF group and was positively correlated with sulfur/thiosulfate respiration, which might have resulted in a higher expression of these pathways in the respective group. Aerobic methane-oxidizing microbial communities, such as Methylobacter, Methylomicrobium, Methylomonas, and Methylosoma, constituted a dominant part of the LVF and CSF groups, except for the YNH-A and YNH-B (Yang-Nyu-Hu) sites. The WST-7 and JS sites were abundant in both methane-producing and methane-oxidizing microbial communities. The LGH-F1 (Lei-Gong-Huo) site was dominated by both methanotrophic and methylotrophic genera, such as Methylomicrobium and Methylophaga, respectively. Methylotrophy, methanotrophs, and hydrocarbon-degrading pathways were more abundant in the LVF and CSF groups but not in the remaining groups. The results of this study extend our knowledge of the diversity, abundance, and metabolic functions of prokaryotes in major terrestrial mud volcanoes in Taiwan.
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Affiliation(s)
- Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien, Taiwan; Department of Psychiatry, Tzu Chi General Hospital, Hualien, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung, Taiwan
| | - Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Rajendran Senthil Kumar
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Hung-Chun Chao
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Centre for Innovative on Aging Society, National Chung Cheng University, Chiayi County, Taiwan.
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7
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Beliaeva M, Seebeck FP. Discovery and Characterization of the Metallopterin-Dependent Ergothioneine Synthase from Caldithrix abyssi. JACS AU 2022; 2:2098-2107. [PMID: 36186560 PMCID: PMC9516567 DOI: 10.1021/jacsau.2c00365] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 05/29/2023]
Abstract
Ergothioneine is a histidine derivative with a 2-mercaptoimidazole side chain and a trimethylated α-amino group. Although the physiological function of this natural product is not yet understood, the facts that many bacteria, some archaea, and most fungi produce ergothioneine and that plants and animals have specific mechanisms to absorb and distribute ergothioneine in specific tissues suggest a fundamental role in cellular life. The observation that ergothioneine biosynthesis has emerged multiple times in molecular evolution points to the same conclusion. Aerobic bacteria and fungi attach sulfur to the imidazole ring of trimethylhistidine via an O2-dependent reaction that is catalyzed by a mononuclear non-heme iron enzyme. Green sulfur bacteria and archaea use a rhodanese-like sulfur transferase to attach sulfur via oxidative polar substitution. In this report, we describe a third unrelated class of enzymes that catalyze sulfur transfer in ergothioneine production. The metallopterin-dependent ergothioneine synthase from Caldithrix abyssi contains an N-terminal module that is related to the tungsten-dependent acetylene hydratase and a C-terminal domain that is a functional cysteine desulfurase. The two modules cooperate to transfer sulfur from cysteine onto trimethylhistidine. Inactivation of the C-terminal desulfurase blocks ergothioneine production but maintains the ability of the metallopterin to exchange sulfur between ergothioneine and trimethylhistidine. Homologous bifunctional enzymes are encoded exclusively in anaerobic bacterial and archaeal species.
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Affiliation(s)
- Mariia
A. Beliaeva
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4002 Basel, Switzerland
- Molecular
Systems Engineering, National Competence
Center in Research (NCCR), 4058 Basel, Switzerland
| | - Florian P. Seebeck
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4002 Basel, Switzerland
- Molecular
Systems Engineering, National Competence
Center in Research (NCCR), 4058 Basel, Switzerland
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8
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Khot V, Zorz J, Gittins DA, Chakraborty A, Bell E, Bautista MA, Paquette AJ, Hawley AK, Novotnik B, Hubert CRJ, Strous M, Bhatnagar S. CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation. Front Microbiol 2022; 12:764058. [PMID: 35069469 PMCID: PMC8767102 DOI: 10.3389/fmicb.2021.764058] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/08/2021] [Indexed: 02/04/2023] Open
Abstract
Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Here we present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate its application in analyzing high-throughput sequence data by predicting hydrocarbon utilization in large metagenomic datasets from diverse environments. CANT-HYD is available at https://github.com/dgittins/CANT-HYD-HydrocarbonBiodegradation.
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Affiliation(s)
- Varada Khot
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Jackie Zorz
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Daniel A Gittins
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Anirban Chakraborty
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Emma Bell
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - María A Bautista
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Alexandre J Paquette
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Alyse K Hawley
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Breda Novotnik
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Casey R J Hubert
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Marc Strous
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Srijak Bhatnagar
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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9
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Grinter R, Greening C. Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea. FEMS Microbiol Rev 2021; 45:fuab021. [PMID: 33851978 PMCID: PMC8498797 DOI: 10.1093/femsre/fuab021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway; however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.
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Affiliation(s)
- Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Chris Greening
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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10
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A Comparative Analysis of Aquatic and Polyethylene-Associated Antibiotic-Resistant Microbiota in the Mediterranean Sea. BIOLOGY 2021; 10:biology10030200. [PMID: 33800749 PMCID: PMC8001005 DOI: 10.3390/biology10030200] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 12/15/2022]
Abstract
In this study, we evaluated the microbiome and the resistome profile of water and fragments of polyethylene (PE) waste collected at the same time from a stream and the seawater in a coastal area of Northwestern Sicily. Although a core microbiome was determined by sequencing of the V3-V4 region of the bacterial 16S rDNA gene, quantitative differences were found among the microbial communities on PE waste and the corresponding water samples. Our findings indicated that PE waste contains a more abundant and increased core microbiome diversity than the corresponding water samples. Moreover, PCR analysis of specific antibiotic resistance genes (ARGs) showed that PE waste harbors more ARGs than the water samples. Thus, PE waste could act as a carrier of antibiotic-resistant microbiota, representing an increased danger for the marine environment and living organisms, as well.
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11
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Dong J, Quan Q, Zhao D, Li C, Zhang C, Chen H, Fang J, Wang L, Liu J. A combined method for the source apportionment of sediment organic carbon in rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 752:141840. [PMID: 32889276 DOI: 10.1016/j.scitotenv.2020.141840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Organic carbon sources apportionment in river sediments is crucial to the output management of organic carbon. We conducted a source apportionment of sediment organic carbon in four rivers in Shaanxi Province, China, with a novel method that combined environmental scanning electron microscopy and energy dispersive X-ray spectrometry (ESEM-EDAX), principal component analysis (PCA), 16S rRNA sequencing, microbial community metabolic prediction, and positive matrix factorization (PMF). According to the ESEM-EDAX results, the sources of light fraction organic carbon (LFOC) were the vegetation residues and the organic carbon adsorbed on them; and the source of heavy fraction organic carbon (HFOC) was organic carbon wrapped in particles. Moreover, 16S rRNA sequencing results of LFOC and HFOC concerning microbes demonstrated that LFOC was mainly composed of carbohydrate, cellulose, and alky-aromatic compounds, and that carbohydrate with high molecular weight might be a part of HFOC. Based on the results of microbial community metabolic prediction, PCA, and PMF, we found dissolved organic carbon (DOC) was mainly from lipopolysaccharide biosynthesis, apoptosis, and decomposition of carboxylic acids. And it might be mainly composed of lipopolysaccharide, carbohydrates, and organic acid with low molecular. To reflect the appearance of a specific DOC type, three biomarkers were proposed based on the microbial relative abundance and specificity. This research proposed a new method to trace the sources of organic carbon and established microbial biomarkers for the appearance of specific DOC, which would promote the understanding of organic carbon sources into microbes. Thus, this research provides new perspectives in the source apportionment and the life cycle of organic carbon in rivers.
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Affiliation(s)
- Junyu Dong
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Quan Quan
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China
| | - Di Zhao
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Changchao Li
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Chao Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Hao Chen
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Jiaohui Fang
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Lifei Wang
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Jian Liu
- Environment Research Institute, Shandong University, Qingdao 266237, China.
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Mullin SW, Wanger G, Kruger BR, Sackett JD, Hamilton-Brehm SD, Bhartia R, Amend JP, Moser DP, Orphan VJ. Patterns of in situ Mineral Colonization by Microorganisms in a ~60°C Deep Continental Subsurface Aquifer. Front Microbiol 2020; 11:536535. [PMID: 33329414 PMCID: PMC7711152 DOI: 10.3389/fmicb.2020.536535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 09/24/2020] [Indexed: 11/13/2022] Open
Abstract
The microbial ecology of the deep biosphere is difficult to characterize, owing in part to sampling challenges and poorly understood response mechanisms to environmental change. Pre-drilled wells, including oil wells or boreholes, offer convenient access, but sampling is frequently limited to the water alone, which may provide only a partial view of the native diversity. Mineral heterogeneity demonstrably affects colonization by deep biosphere microorganisms, but the connections between the mineral-associated and planktonic communities remain unclear. To understand the substrate effects on microbial colonization and the community response to changes in organic carbon, we conducted an 18-month series of in situ experiments in a warm (57°C), anoxic, fractured carbonate aquifer at 752 m depth using replicate open, screened cartridges containing different solid substrates, with a proteinaceous organic matter perturbation halfway through this series. Samples from these cartridges were analyzed microscopically and by Illumina (iTag) 16S rRNA gene libraries to characterize changes in mineralogy and the diversity of the colonizing microbial community. The substrate-attached and planktonic communities were significantly different in our data, with some taxa (e.g., Candidate Division KB-1) rare or undetectable in the first fraction and abundant in the other. The substrate-attached community composition also varied significantly with mineralogy, such as with two Rhodocyclaceae OTUs, one of which was abundant on carbonate minerals and the other on silicic substrates. Secondary sulfide mineral formation, including iron sulfide framboids, was observed on two sets of incubated carbonates. Notably, microorganisms were attached to the framboids, which were correlated with abundant Sulfurovum and Desulfotomaculum sp. sequences in our analysis. Upon organic matter perturbation, mineral-associated microbial diversity differences were temporarily masked by the dominance of putative heterotrophic taxa in all samples, including OTUs identified as Caulobacter, Methyloversatilis, and Pseudomonas. Subsequent experimental deployments included a methanogen-dominated stage (Methanobacteriales and Methanomicrobiales) 6 months after the perturbation and a return to an assemblage similar to the pre-perturbation community after 9 months. Substrate-associated community differences were again significant within these subsequent phases, however, demonstrating the value of in situ time course experiments to capture a fraction of the microbial assemblage that is frequently difficult to observe in pre-drilled wells.
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Affiliation(s)
- Sean W Mullin
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Greg Wanger
- Jet Propulsion Laboratory, Pasadena, CA, United States
| | - Brittany R Kruger
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, United States
| | - Joshua D Sackett
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, United States
| | - Scott D Hamilton-Brehm
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, United States
| | - Rohit Bhartia
- Jet Propulsion Laboratory, Pasadena, CA, United States
| | - Jan P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Duane P Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, United States
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
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Gut Microbiome in Children from Indigenous and Urban Communities in México: Different Subsistence Models, Different Microbiomes. Microorganisms 2020; 8:microorganisms8101592. [PMID: 33081076 PMCID: PMC7602701 DOI: 10.3390/microorganisms8101592] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
The human gut microbiome is an important component that defines host health. Childhood is a particularly important period for the establishment and development of gut microbiota (GM). We sequenced the 16S rRNA gene from fecal samples of children between 5 and 10 years old, in two Mexican communities with contrasting lifestyles, i.e., “Westernized” (México City, n = 13) and “non-Westernized” (Me’phaa indigenous group, n = 29), in order to characterize and compare their GM. The main differences between these two communities were in bacteria associated with different types of diets (high animal protein and refined sugars vs. high fiber food, respectively). In addition, the GM of Me’phaa children showed higher total diversity and the presence of exclusive phyla, such as Deinococcus-Thermus, Chloroflexi, Elusimicrobia, Acidobacteria, and Fibrobacteres. In contrast, the children from México City showed less diversity and the presence of Saccharibacteria phylum, which was associated with the degradation of sugar compounds and was not present in the samples from Me’phaa children. This comparison provided further knowledge of the selective pressures affecting microbial ecosystemic composition over the course of human evolution and the potential consequences of pathophysiological states correlated with Westernization lifestyles.
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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Microbial community profiling of ammonia and nitrite oxidizing bacterial enrichments from brackishwater ecosystems for mitigating nitrogen species. Sci Rep 2020; 10:5201. [PMID: 32251334 PMCID: PMC7090006 DOI: 10.1038/s41598-020-62183-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 03/10/2020] [Indexed: 11/25/2022] Open
Abstract
Nitrogen species such as ammonia and nitrite are considered as major stressors in modern aquaculture practices. We developed enrichments of ammonia oxidising bacteria (AOB) and nitrite oxidising bacteria (NOB) for effective mitigation of nitrogenous wastes in the shrimp culture operations. The objective of this study was to understand the microbial community composition of AOB and NOB enrichments using the V3-V4 region of the 16S rDNA gene by Illumina MiSeq sequencing. The analysis revealed 2948 and 1069 OTUs at 97% similarity index and Shannon alpha diversity index of 7.64 and 4.85 for AOB and NOB enrichments, respectively. Comparative analysis showed that a total of 887 OTUs were common among AOB and NOB enrichments. The AOB and NOB enrichment were dominated by Eubacteria at 96% and 99.7% respectively. Proteobacterial phylum constituted 31.46% (AOB) and 39.75% (NOB) and dominated by α-Proteobacteria (20%) in AOB and γ-Proteobacteria (16%) in NOB. Among the species in AOB enrichment (2,948) two sequences were assigned to ammonia oxidising bacterial group belonging to Nitrosomonas, and Nitrosococcus genera and two belonged to archaeon group comprising Nitrosopumilus and Candidatus Nitrososphaeraea genera. The NOB enrichment was predominated by Nitrospiraceae and Thermodesulfovibrionaceae. Further, the data revealed the presence of heterotrophic bacteria contributing to the process of nitrification and form microcosm with the AOB and NOB. PICRUSt analysis predicted the presence of 24 different nitrogen cycling genes involved in nitrification, denitrification, ammonia and nitrogen transporter family, nitrate reduction and ammonia assimilation. The study confirms the presence of many lesser known nitrifying bacteria along with well characterised nitrifiers.
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