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Degli Esposti M, Guerrero G, Rogel MA, Issotta F, Rojas-Villalobos C, Quatrini R, Martinez-Romero E. The phylogeny of Acetobacteraceae: photosynthetic traits and deranged respiratory enzymes. Microbiol Spectr 2023; 11:e0057523. [PMID: 37975678 PMCID: PMC10715153 DOI: 10.1128/spectrum.00575-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 09/21/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Acetobacteraceae are one of the best known and most extensively studied groups of bacteria, which nowadays encompasses a variety of taxa that are very different from the vinegar-producing species defining the family. Our paper presents the most detailed phylogeny of all current taxa classified as Acetobacteraceae, for which we propose a taxonomic revision. Several of such taxa inhabit some of the most extreme environments on the planet, from the deserts of Antarctica to the Sinai desert, as well as acidic niches in volcanic sites like the one we have been studying in Patagonia. Our work documents the progressive variation of the respiratory chain in early branching Acetobacteraceae into the different respiratory chains of acidophilic taxa such as Acidocella and acetous taxa such as Acetobacter. Remarkably, several genomes retain remnants of ancestral photosynthetic traits and functional bc 1 complexes. Thus, we propose that the common ancestor of Acetobacteraceae was photosynthetic.
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Affiliation(s)
- Mauro Degli Esposti
- Center for Genomic Sciences, UNAM Campus de Morelos, Cuernavaca, Morelos, Mexico
| | - Gabriela Guerrero
- Center for Genomic Sciences, UNAM Campus de Morelos, Cuernavaca, Morelos, Mexico
| | - Marco A. Rogel
- Center for Genomic Sciences, UNAM Campus de Morelos, Cuernavaca, Morelos, Mexico
| | - Francisco Issotta
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia y Vida, Huechuraba, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, P. Universidad Católica, Santiago, Chile
| | - Camila Rojas-Villalobos
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia y Vida, Huechuraba, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Raquel Quatrini
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia y Vida, Huechuraba, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Providencia, Santiago, Chile
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Demergasso C, Neilson JW, Tebes-Cayo C, Véliz R, Ayma D, Laubitz D, Barberán A, Chong-Díaz G, Maier RM. Hyperarid soil microbial community response to simulated rainfall. Front Microbiol 2023; 14:1202266. [PMID: 37779711 PMCID: PMC10537920 DOI: 10.3389/fmicb.2023.1202266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/31/2023] [Indexed: 10/03/2023] Open
Abstract
The exceptionally long and protracted aridity in the Atacama Desert (AD), Chile, provides an extreme, terrestrial ecosystem that is ideal for studying microbial community dynamics under hyperarid conditions. Our aim was to characterize the temporal response of hyperarid soil AD microbial communities to ex situ simulated rainfall (5% g water/g dry soil for 4 weeks) without nutrient amendment. We conducted replicated microcosm experiments with surface soils from two previously well-characterized AD hyperarid locations near Yungay at 1242 and 1609 masl (YUN1242 and YUN1609) with distinct microbial community compositions and average soil relative humidity levels of 21 and 17%, respectively. The bacterial and archaeal response to soil wetting was evaluated by 16S rRNA gene qPCR, and amplicon sequencing. Initial YUN1242 bacterial and archaeal 16S rRNA gene copy numbers were significantly higher than for YUN1609. Over the next 4 weeks, qPCR results showed significant increases in viable bacterial abundance, whereas archaeal abundance decreased. Both communities were dominated by 10 prokaryotic phyla (Actinobacteriota, Proteobacteria, Chloroflexota, Gemmatimonadota, Firmicutes, Bacteroidota, Planctomycetota, Nitrospirota, Cyanobacteriota, and Crenarchaeota) but there were significant site differences in the relative abundances of Gemmatimonadota and Chloroflexota, and specific actinobacterial orders. The response to simulated rainfall was distinct for the two communities. The actinobacterial taxa in the YUN1242 community showed rapid changes while the same taxa in the YUN1609 community remained relatively stable until day 30. Analysis of inferred function of the YUN1242 microbiome response implied an increase in the relative abundance of known spore-forming taxa with the capacity for mixotrophy at the expense of more oligotrophic taxa, whereas the YUN1609 community retained a stable profile of oligotrophic, facultative chemolithoautotrophic and mixotrophic taxa. These results indicate that bacterial communities in extreme hyperarid soils have the capacity for growth in response to simulated rainfall; however, historic variations in long-term hyperaridity exposure produce communities with distinct putative metabolic capacities.
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Affiliation(s)
- Cecilia Demergasso
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
| | - Julia W. Neilson
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Cinthya Tebes-Cayo
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
- Department of Geology, Faculty of Engineering and Geological Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Roberto Véliz
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
| | - Diego Ayma
- Department of Mathematics, Faculty of Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Daniel Laubitz
- Steele Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, United States
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Guillermo Chong-Díaz
- Department of Geology, Faculty of Engineering and Geological Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Raina M. Maier
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
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Hessler T, Huddy RJ, Sachdeva R, Lei S, Harrison STL, Diamond S, Banfield JF. Vitamin interdependencies predicted by metagenomics-informed network analyses and validated in microbial community microcosms. Nat Commun 2023; 14:4768. [PMID: 37553333 PMCID: PMC10409787 DOI: 10.1038/s41467-023-40360-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/20/2023] [Indexed: 08/10/2023] Open
Abstract
Metagenomic or metabarcoding data are often used to predict microbial interactions in complex communities, but these predictions are rarely explored experimentally. Here, we use an organism abundance correlation network to investigate factors that control community organization in mine tailings-derived laboratory microbial consortia grown under dozens of conditions. The network is overlaid with metagenomic information about functional capacities to generate testable hypotheses. We develop a metric to predict the importance of each node within its local network environments relative to correlated vitamin auxotrophs, and predict that a Variovorax species is a hub as an important source of thiamine. Quantification of thiamine during the growth of Variovorax in minimal media show high levels of thiamine production, up to 100 mg/L. A few of the correlated thiamine auxotrophs are predicted to produce pantothenate, which we show is required for growth of Variovorax, supporting that a subset of vitamin-dependent interactions are mutualistic. A Cryptococcus yeast produces the B-vitamin pantothenate, and co-culturing with Variovorax leads to a 90-130-fold fitness increase for both organisms. Our study demonstrates the predictive power of metagenome-informed, microbial consortia-based network analyses for identifying microbial interactions that underpin the structure and functioning of microbial communities.
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Affiliation(s)
- Tomas Hessler
- The Innovative Genomics Institute at the University of California, Berkeley, CA, USA
- The Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robert J Huddy
- Reasearch Office, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Rohan Sachdeva
- The Innovative Genomics Institute at the University of California, Berkeley, CA, USA
- The Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Shufei Lei
- The Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Susan T L Harrison
- The Center for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa
- The Future Water Institute, University of Cape Town, Cape Town, South Africa
- Department of Chemical Engineering, University of Cape Town, Cape Town, South Africa
| | - Spencer Diamond
- The Innovative Genomics Institute at the University of California, Berkeley, CA, USA
- The Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- The Innovative Genomics Institute at the University of California, Berkeley, CA, USA.
- The Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- The Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
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Ascandari A, Aminu S, Safdi NEH, El Allali A, Daoud R. A bibliometric analysis of the global impact of metaproteomics research. Front Microbiol 2023; 14:1217727. [PMID: 37476667 PMCID: PMC10354264 DOI: 10.3389/fmicb.2023.1217727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023] Open
Abstract
Background Metaproteomics is a subfield in meta-omics that is used to characterize the proteome of a microbial community. Despite its importance and the plethora of publications in different research area, scientists struggle to fully comprehend its functional impact on the study of microbiomes. In this study, bibliometric analyses are used to evaluate the current state of metaproteomic research globally as well as evaluate the specific contribution of Africa to this burgeoning research area. In this study, we use bibliometric analyses to evaluate the current state of metaproteomic research globally, identify research frontiers and hotspots, and further predict future trends in metaproteomics. The specific contribution of Africa to this research area was evaluated. Methods Relevant documents from 2004 to 2022 were extracted from the Scopus database. The documents were subjected to bibliometric analyses and visualization using VOS viewer and Biblioshiny package in R. Factors such as the trends in publication, country and institutional cooperation networks, leading scientific journals, author's productivity, and keywords analyses were conducted. The African publications were ranked using Field-Weighted Citation Impact (FWCI) scores. Results A total of 1,138 documents were included and the number of publications increased drastically from 2004 to 2022 with more publications (170) reported in 2021. In terms of publishers, Frontiers in Microbiology had the highest number of total publications (62). The United States of America (USA), Germany, China, and Canada, together with other European countries were the most productive. Institution-wise, the Helmholtz Zentrum für Umweltforschung, Germany had more publications while Max Plank Institute had the highest total collaborative link strength. Jehmlich N. was the most productive author whereas Hettich RL had the highest h-index of 63. Regarding Africa, only 2.2% of the overall publications were from the continent with more publication outputs from South Africa. More than half of the publications from the continent had an FWCI score ≥ 1. Conclusion The scientific outputs of metaproteomics are rapidly evolving with developed countries leading the way. Although Africa showed prospects for future progress, this could only be accelerated by providing funding, increased collaborations, and mentorship programs.
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Affiliation(s)
- AbdulAziz Ascandari
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Suleiman Aminu
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Nour El Houda Safdi
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Rachid Daoud
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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Sun A, Li CP, Chen Z, Zhang S, Li DY, Yang Y, Li LQ, Zhao Y, Wang K, Li Z, Liu J, Liu S, Wang J, Liu JJG. The compact Casπ (Cas12l) 'bracelet' provides a unique structural platform for DNA manipulation. Cell Res 2023; 33:229-244. [PMID: 36650285 PMCID: PMC9977741 DOI: 10.1038/s41422-022-00771-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 12/22/2022] [Indexed: 01/19/2023] Open
Abstract
CRISPR-Cas modules serve as the adaptive nucleic acid immune systems for prokaryotes, and provide versatile tools for nucleic acid manipulation in various organisms. Here, we discovered a new miniature type V system, CRISPR-Casπ (Cas12l) (~860 aa), from the environmental metagenome. Complexed with a large guide RNA (~170 nt) comprising the tracrRNA and crRNA, Casπ (Cas12l) recognizes a unique 5' C-rich PAM for DNA cleavage under a broad range of biochemical conditions, and generates gene editing in mammalian cells. Cryo-EM study reveals a 'bracelet' architecture of Casπ effector encircling the DNA target at 3.4 Å resolution, substantially different from the canonical 'two-lobe' architectures of Cas12 and Cas9 nucleases. The large guide RNA serves as a 'two-arm' scaffold for effector assembly. Our study expands the knowledge of DNA targeting mechanisms by CRISPR effectors, and offers an efficient but compact platform for DNA manipulation.
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Affiliation(s)
- Ao Sun
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Cheng-Ping Li
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhihang Chen
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shouyue Zhang
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Dan-Yuan Li
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yun Yang
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Long-Qi Li
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuqian Zhao
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Kaichen Wang
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhaofu Li
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jinxia Liu
- Department of Environmental Engineering, Peking University, Beijing, China
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing, China
| | - Sitong Liu
- Department of Environmental Engineering, Peking University, Beijing, China
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing, China
| | - Jia Wang
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Jun-Jie Gogo Liu
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
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Roux S, Fischer MG, Hackl T, Katz LA, Schulz F, Yutin N. Updated Virophage Taxonomy and Distinction from Polinton-like Viruses. Biomolecules 2023; 13:204. [PMID: 36830574 PMCID: PMC9952930 DOI: 10.3390/biom13020204] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of "hyperparasitism" in the viral world. While only a handful of virophages have been isolated, a vast diversity of virophage-like sequences have been uncovered from diverse metagenomes. Their wide ecological distribution, idiosyncratic infection and replication strategy, ability to integrate into protist and giant virus genomes and potential role in antiviral defense have made virophages a topic of broad interest. However, one limitation for further studies is the lack of clarity regarding the nomenclature and taxonomy of this group of viruses. Specifically, virophages have been linked in the literature to other "virophage-like" mobile genetic elements and viruses, including polinton-like viruses (PLVs), but there are no formal demarcation criteria and proper nomenclature for either group, i.e., virophage or PLVs. Here, as part of the ICTV Virophage Study Group, we leverage a large set of genomes gathered from published datasets as well as newly generated protist genomes to propose delineation criteria and classification methods at multiple taxonomic ranks for virophages 'sensu stricto', i.e., genomes related to the prototype isolates Sputnik and mavirus. Based on a combination of comparative genomics and phylogenetic analyses, we show that this group of virophages forms a cohesive taxon that we propose to establish at the class level and suggest a subdivision into four orders and seven families with distinctive ecogenomic features. Finally, to illustrate how the proposed delineation criteria and classification method would be used, we apply these to two recently published datasets, which we show include both virophages and other virophage-related elements. Overall, we see this proposed classification as a necessary first step to provide a robust taxonomic framework in this area of the virosphere, which will need to be expanded in the future to cover other virophage-related viruses such as PLVs.
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Affiliation(s)
- Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthias G. Fischer
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, 69120 Heidelberg, Germany
| | - Thomas Hackl
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Wang L, An X, Xiao X, Li N, Xie D, Lai F, Zhang Q. Treatment of thiocyanate-containing wastewater: a critical review of thiocyanate destruction in industrial effluents. World J Microbiol Biotechnol 2022; 39:35. [PMID: 36469179 DOI: 10.1007/s11274-022-03481-4] [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: 10/18/2022] [Accepted: 11/23/2022] [Indexed: 12/09/2022]
Abstract
Thiocyanate is a common pollutant in gold mine, textile, printing, dyeing, coking and other industries. Therefore, thiocyanate in industrial wastewater is an urgent problem to be solved. This paper reviews the chemical properties, applications, sources and toxicity of thiocyanate, as well as the various treatment methods for thiocyanate in wastewater and their advantages and disadvantages. It is emphasized that biological systems, ranging from laboratory to full-scale, are able to successfully remove thiocyanate from factories. Thiocyanate-degrading microorganisms degrade thiocyanate in autotrophic manner for energy, while other biodegrading microorganisms use thiocyanate as a carbon or nitrogen source, and the biochemical pathways and enzymes involved in thiocyanate metabolism by different bacteria are discussed in detail. In the future, degradation mechanisms should be investigated at the molecular level, with further research aiming to improve the biochemical understanding of thiocyanate metabolism and scaling up thiocyanate degradation technologies from the laboratory to a full-scale.
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Affiliation(s)
- Liuwei Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Xuejiao An
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Xiaoshuang Xiao
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Ningjian Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Dong Xie
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Fenju Lai
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Qinghua Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
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Liu J, Chu G, Wang Q, Zhang Z, Lu S, She Z, Zhao Y, Jin C, Guo L, Ji J, Gao M. Metagenomic analysis and nitrogen removal performance evaluation of activated sludge from a sequencing batch reactor under different salinities. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 323:116213. [PMID: 36108513 DOI: 10.1016/j.jenvman.2022.116213] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/28/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
The effect of salinity on the nitrogen removal performance and microbial community of activated sludge was investigated in a sequencing batch reactor. The NH4+-N removal efficiency was over 95% at 0-4% salinity, indicating that the nitrification performance of activated sludge was slightly affected by lower salinity. The obvious nitrite accumulation was observed with the increment of the salinity to 5%, followed by a notable decline in the nitrogen removal performance at 6% salinity. The salinity inhibited the microbial activity, and the specific rate of nitrification and denitrification was decreased by the increasing salinity obviously. Additionally, the lower activity of superoxide dismutase and peroxidase and higher reactive oxygen species content in activated sludge might account for the deteriorative nitrogen removal performance at 6% salinity. Metagenomics analysis revealed that the genes encoding the ABC-type quaternary amine transporter in the ABC transporter pathway were abundant in the activated sludge at 2% and 4% salinity, and the higher salinity of 6% led to the loss of the genes encoding the p-type Na+ transporter in the ABC transporter pathway. These results indicated that the salinity could weaken the ABC transporter pathway for the balance of osmotic pressure in activated sludge. The microbial activity and nitrogen removal performance of activated sludge were decreased due to the unbalanced osmotic pressure at higher salinity.
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Affiliation(s)
- Jiateng Liu
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering, Qingdao, 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Guangyu Chu
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Qianzhi Wang
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Zhiming Zhang
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China.
| | - Shuailing Lu
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Zonglian She
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Yangguo Zhao
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Chunji Jin
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Liang Guo
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Junyuan Ji
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Mengchun Gao
- Key Lab of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering, Qingdao, 266100, China.
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9
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Wang C, Liu Y, Huang M, Xiang W, Wang Z, Wu X, Zan F, Zhou T. A rational strategy of combining Fenton oxidation and biological processes for efficient nitrogen removal in toxic coking wastewater. BIORESOURCE TECHNOLOGY 2022; 363:127897. [PMID: 36075350 DOI: 10.1016/j.biortech.2022.127897] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Effective removal of nitrogen from coking wastewaters is a great challenge, since conventional biological technologies commonly suffer from concentrated bio-toxic components such as phenolic compounds and thiocyanide (SCN-). This study has successfully developed a novel ternary process for efficiently removing nitrogen from a practical coking wastewater, by rationally combined biological pretreatment, Fenton sub-pretreatment and final partial nitrification-denitrification (PN) process. It was noted that the oxic biological pretreatment (OP) could degrade above 80 % of COD and SCN- in the wastewater, by adopting the pristine coking wastewater sludge. Fenton sub-pretreatment would further degrade the residual toxic organics and protect the metabolic activity of nitrobacteria and denitrobacteria, realizing the efficient removal of NH4+-N and TN that occurred in the final PN process with self-cultivated sludge. This work can provide an interesting strategy by rationally combining biological-physicochemical processes for nitrogen removal in toxic industrial wastewaters.
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Affiliation(s)
- Chen Wang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Yaming Liu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Mingjie Huang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, PR China; CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Wei Xiang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Zhicheng Wang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Xiaohui Wu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Feixiang Zan
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, PR China; Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, PR China
| | - Tao Zhou
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, PR China.
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10
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Urbaitis T, Gasiunas G, Young JK, Hou Z, Paulraj S, Godliauskaite E, Juskeviciene MM, Stitilyte M, Jasnauskaite M, Mabuchi M, Robb GB, Siksnys V. A new family of CRISPR-type V nucleases with C-rich PAM recognition. EMBO Rep 2022; 23:e55481. [PMID: 36268581 PMCID: PMC9724661 DOI: 10.15252/embr.202255481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 12/12/2022] Open
Abstract
Most CRISPR-type V nucleases are stimulated to cleave double-stranded (ds) DNA targets by a T-rich PAM, which restricts their targeting range. Here, we identify and characterize a new family of type V RNA-guided nuclease, Cas12l, that exclusively recognizes a C-rich (5'-CCY-3') PAM. The organization of genes within its CRISPR locus is similar to type II-B CRISPR-Cas9 systems, but both sequence analysis and functional studies establish it as a new family of type V effector. Biochemical experiments show that Cas12l nucleases function optimally between 37 and 52°C, depending on the ortholog, and preferentially cut supercoiled DNA. Like other type V nucleases, it exhibits collateral nonspecific ssDNA and ssRNA cleavage activity that is triggered by ssDNA or dsDNA target recognition. Finally, we show that one family member, Asp2Cas12l, functions in a heterologous cellular environment, altogether, suggesting that this new group of CRISPR-associated nucleases may be harnessed as genome editing reagents.
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Affiliation(s)
- Tomas Urbaitis
- CasZymeVilniusLithuania,Institute of BiotechnologyVilnius UniversityVilniusLithuania
| | | | | | - Zhenglin Hou
- Farming Solutions & DigitalCorteva Agriscience™JohnstonIAUSA
| | | | | | | | - Migle Stitilyte
- CasZymeVilniusLithuania,Institute of BiotechnologyVilnius UniversityVilniusLithuania
| | - Monika Jasnauskaite
- CasZymeVilniusLithuania,Present address:
LSC‐EMBL Partnership Institute for Genome Technologies Editing, Life Sciences CenterVilnius UniversityVilniusLithuania
| | | | | | - Virginijus Siksnys
- CasZymeVilniusLithuania,Institute of BiotechnologyVilnius UniversityVilniusLithuania
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11
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Köstlbacher S, Collingro A, Halter T, Schulz F, Jungbluth SP, Horn M. Pangenomics reveals alternative environmental lifestyles among chlamydiae. Nat Commun 2021; 12:4021. [PMID: 34188040 PMCID: PMC8242063 DOI: 10.1038/s41467-021-24294-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/10/2021] [Indexed: 02/07/2023] Open
Abstract
Chlamydiae are highly successful strictly intracellular bacteria associated with diverse eukaryotic hosts. Here we analyzed metagenome-assembled genomes of the "Genomes from Earth's Microbiomes" initiative from diverse environmental samples, which almost double the known phylogenetic diversity of the phylum and facilitate a highly resolved view at the chlamydial pangenome. Chlamydiae are defined by a relatively large core genome indicative of an intracellular lifestyle, and a highly dynamic accessory genome of environmental lineages. We observe chlamydial lineages that encode enzymes of the reductive tricarboxylic acid cycle and for light-driven ATP synthesis. We show a widespread potential for anaerobic energy generation through pyruvate fermentation or the arginine deiminase pathway, and we add lineages capable of molecular hydrogen production. Genome-informed analysis of environmental distribution revealed lineage-specific niches and a high abundance of chlamydiae in some habitats. Together, our data provide an extended perspective of the variability of chlamydial biology and the ecology of this phylum of intracellular microbes.
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Affiliation(s)
- Stephan Köstlbacher
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Astrid Collingro
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Tamara Halter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | | | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
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12
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Huddy RJ, Sachdeva R, Kadzinga F, Kantor RS, Harrison STL, Banfield JF. Thiocyanate and Organic Carbon Inputs Drive Convergent Selection for Specific Autotrophic Afipia and Thiobacillus Strains Within Complex Microbiomes. Front Microbiol 2021; 12:643368. [PMID: 33897653 PMCID: PMC8061750 DOI: 10.3389/fmicb.2021.643368] [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: 12/18/2020] [Accepted: 03/09/2021] [Indexed: 01/14/2023] Open
Abstract
Thiocyanate (SCN–) contamination threatens aquatic ecosystems and pollutes vital freshwater supplies. SCN–-degrading microbial consortia are commercially adapted for remediation, but the impact of organic amendments on selection within SCN–-degrading microbial communities has not been investigated. Here, we tested whether specific strains capable of degrading SCN– could be reproducibly selected for based on SCN– loading and the presence or absence of added organic carbon. Complex microbial communities derived from those used to treat SCN–-contaminated water were exposed to systematically increased input SCN concentrations in molasses-amended and -unamended reactors and in reactors switched to unamended conditions after establishing the active SCN–-degrading consortium. Five experiments were conducted over 790 days, and genome-resolved metagenomics was used to resolve community composition at the strain level. A single Thiobacillus strain proliferated in all reactors at high loadings. Despite the presence of many Rhizobiales strains, a single Afipia variant dominated the molasses-free reactor at moderately high loadings. This strain is predicted to break down SCN– using a novel thiocyanate desulfurase, oxidize resulting reduced sulfur, degrade product cyanate to ammonia and CO2 via cyanate hydratase, and fix CO2 via the Calvin–Benson–Bassham cycle. Removal of molasses from input feed solutions reproducibly led to dominance of this strain. Although sustained by autotrophy, reactors without molasses did not stably degrade SCN– at high loading rates, perhaps due to loss of biofilm-associated niche diversity. Overall, convergence in environmental conditions led to convergence in the strain composition, although reactor history also impacted the trajectory of community compositional change.
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Affiliation(s)
- Robert J Huddy
- Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa.,Future Water Institute, University of Cape Town, Cape Town, South Africa
| | - Rohan Sachdeva
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Fadzai Kadzinga
- Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa.,Future Water Institute, University of Cape Town, Cape Town, South Africa
| | - Rose S Kantor
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States
| | - Susan T L Harrison
- Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa.,Future Water Institute, University of Cape Town, Cape Town, South Africa
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States.,Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States.,School of Earth Sciences, University of Melbourne, Melbourne, VIC, Australia
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13
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Shafiei F, Watts MP, Pajank L, Moreau JW. The effect of heavy metals on thiocyanate biodegradation by an autotrophic microbial consortium enriched from mine tailings. Appl Microbiol Biotechnol 2020; 105:417-427. [PMID: 33263791 PMCID: PMC7778618 DOI: 10.1007/s00253-020-10983-4] [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: 06/16/2020] [Revised: 10/17/2020] [Accepted: 10/26/2020] [Indexed: 11/28/2022]
Abstract
Abstract Bioremediation systems represent an environmentally sustainable approach to degrading industrially generated thiocyanate (SCN−), with low energy demand and operational costs and high efficiency and substrate specificity. However, heavy metals present in mine tailings effluent may hamper process efficiency by poisoning thiocyanate-degrading microbial consortia. Here, we experimentally tested the tolerance of an autotrophic SCN−-degrading bacterial consortium enriched from gold mine tailings for Zn, Cu, Ni, Cr, and As. All of the selected metals inhibited SCN− biodegradation to different extents, depending on concentration. At pH of 7.8 and 30 °C, complete inhibition of SCN− biodegradation by Zn, Cu, Ni, and Cr occurred at 20, 5, 10, and 6 mg L−1, respectively. Lower concentrations of these metals decreased the rate of SCN− biodegradation, with relatively long lag times. Interestingly, the microbial consortium tolerated As even at 500 mg L−1, although both the rate and extent of SCN− biodegradation were affected. Potentially, the observed As tolerance could be explained by the origin of our microbial consortium in tailings derived from As-enriched gold ore (arsenopyrite). This study highlights the importance of considering metal co-contamination in bioreactor design and operation for SCN− bioremediation at mine sites. Key points • Both the efficiency and rate of SCN−biodegradation were inhibited by heavy metals, to different degrees depending on type and concentration of metal. • The autotrophic microbial consortium was capable of tolerating high concentrations of As, potential having adapted to higher As levels derived from the tailings source. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-020-10983-4.
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Affiliation(s)
- Farhad Shafiei
- School of Earth Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mathew P Watts
- School of Earth Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Lukas Pajank
- School of Earth Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - John W Moreau
- School of Earth Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia. .,School of Geographical & Earth Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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14
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Acharya SM, Chakraborty R, Tringe SG. Emerging Trends in Biological Treatment of Wastewater From Unconventional Oil and Gas Extraction. Front Microbiol 2020; 11:569019. [PMID: 33013800 PMCID: PMC7509137 DOI: 10.3389/fmicb.2020.569019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/19/2020] [Indexed: 01/16/2023] Open
Abstract
Unconventional oil and gas exploration generates an enormous quantity of wastewater, commonly referred to as flowback and produced water (FPW). Limited freshwater resources and stringent disposal regulations have provided impetus for FPW reuse. Organic and inorganic compounds released from the shale/brine formation, microbial activity, and residual chemicals added during hydraulic fracturing bestow a unique as well as temporally varying chemical composition to this wastewater. Studies indicate that many of the compounds found in FPW are amenable to biological degradation, indicating biological treatment may be a viable option for FPW processing and reuse. This review discusses commonly characterized contaminants and current knowledge on their biodegradability, including the enzymes and organisms involved. Further, a perspective on recent novel hybrid biological treatments and application of knowledge gained from omics studies in improving these treatments is explored.
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Affiliation(s)
- Shwetha M Acharya
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Susannah G Tringe
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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15
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Chen LX, Anantharaman K, Shaiber A, Eren AM, Banfield JF. Accurate and complete genomes from metagenomes. Genome Res 2020; 30:315-333. [PMID: 32188701 PMCID: PMC7111523 DOI: 10.1101/gr.258640.119] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Genomes are an integral component of the biological information about an organism; thus, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures, and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs); but gaps, local assembly errors, chimeras, and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and, in some cases, achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of about 7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. The analysis of cumulative GC skew identified potential misassemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.
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Affiliation(s)
- Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
| | - Karthik Anantharaman
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
| | - Alon Shaiber
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois 60637, USA.,Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA.,Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA.,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA
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16
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Oshiki M, Fukushima T, Kawano S, Kasahara Y, Nakagawa J. Thiocyanate Degradation by a Highly Enriched Culture of the Neutrophilic Halophile Thiohalobacter sp. Strain FOKN1 from Activated Sludge and Genomic Insights into Thiocyanate Metabolism. Microbes Environ 2019; 34:402-412. [PMID: 31631078 PMCID: PMC6934394 DOI: 10.1264/jsme2.me19068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Thiocyanate (SCN-) is harmful to a wide range of organisms, and its removal is essential for environmental protection. A neutrophilic halophile capable of thiocyanate degradation, Thiohalobacter sp. strain FOKN1, was highly enriched (relative abundance; 98.4%) from activated sludge collected from a bioreactor receiving thiocyanate-rich wastewater. The enrichment culture degraded 3.38 mM thiocyanate within 140 h, with maximum activity at pH 8.8, 37°C, and 0.18 M sodium chloride. Thiocyanate degradation was inhibited by 30 mg L-1 phenol, but not by thiosulfate. Microbial thiocyanate degradation is catalyzed by thiocyanate dehydrogenase, while limited information is currently available on the molecular mechanisms underlying thiocyanate degradation by the thiocyanate dehydrogenase of neutrophilic halophiles. Therefore, (meta)genomic and proteomic analyses of enrichment cultures were performed to elucidate the whole genome sequence and proteome of Thiohalobacter sp. strain FOKN1. The 3.23-Mb circular Thiohalobacter sp. strain FOKN1 genome was elucidated using a PacBio RSII sequencer, and the expression of 914 proteins was identified by tandem mass spectrometry. The Thiohalobacter sp. strain FOKN1 genome had a gene encoding thiocyanate dehydrogenase, which was abundant in the proteome, suggesting that thiocyanate is degraded by thiocyanate dehydrogenase to sulfur and cyanate. The sulfur formed may be oxidized to sulfate by the sequential oxidation reactions of dissimilatory sulfite reductase, adenosine-5'-phosphosulfate reductase, and dissimilatory ATP sulfurylase. Although the Thiohalobacter sp. strain FOKN1 genome carried a gene encoding cyanate lyase, its protein expression was not detectable. The present study advances the understanding of the molecular mechanisms underlying thiocyanate degradation by the thiocyanate dehydrogenase of neutrophilic halophiles.
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Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
| | - Toshikazu Fukushima
- Advanced Technology Research Laboratories, Research & Development, Nippon Steel Corporation
| | - Shuichi Kawano
- Department of Computer and Network Engineering Graduate School of Informatics and Engineering, The University of Electro-Communications
| | | | - Junichi Nakagawa
- Advanced Technology Research Laboratories, Research & Development, Nippon Steel Corporation
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17
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Watts MP, Spurr LP, Lê Cao KA, Wick R, Banfield JF, Moreau JW. Genome-resolved metagenomics of an autotrophic thiocyanate-remediating microbial bioreactor consortium. WATER RESEARCH 2019; 158:106-117. [PMID: 31022528 DOI: 10.1016/j.watres.2019.02.058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
Industrial thiocyanate (SCN-) waste streams from gold mining and coal coking have polluted environments worldwide. Modern SCN- bioremediation involves use of complex engineered heterotrophic microbiomes; little attention has been given to the ability of a simple environmental autotrophic microbiome to biodegrade SCN-. Here we present results from a bioreactor experiment inoculated with SCN- -loaded mine tailings, incubated autotrophically, and subjected to a range of environmentally relevant conditions. Genome-resolved metagenomics revealed that SCN- hydrolase-encoding, sulphur-oxidizing autotrophic bacteria mediated SCN- degradation. These microbes supported metabolically-dependent non-SCN--degrading sulphur-oxidizing autotrophs and non-sulphur oxidizing heterotrophs, and "niche" microbiomes developed spatially (planktonic versus sessile) and temporally (across changing environmental parameters). Bioreactor microbiome structures changed significantly with increasing temperature, shifting from Thiobacilli to a novel SCN- hydrolase-encoding gammaproteobacteria. Transformation of carbonyl sulphide (COS), a key intermediate in global biogeochemical sulphur cycling, was mediated by plasmid-hosted CS2 and COS hydrolase genes associated with Thiobacillus, revealing a potential for horizontal transfer of this function. Our work shows that simple native autotrophic microbiomes from mine tailings can be employed for SCN- bioremediation, thus improving the recycling of ore processing waters and reducing the hydrological footprint of mining.
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Affiliation(s)
- Mathew P Watts
- School of Earth Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Liam P Spurr
- School of Earth Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics and School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ryan Wick
- Department of Biochemistry and Molecular Biology, Bio21, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jillian F Banfield
- School of Earth Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - John W Moreau
- School of Earth Sciences, The University of Melbourne, Parkville, VIC 3010, Australia.
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18
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Spurr LP, Watts MP, Gan HM, Moreau JW. Biodegradation of thiocyanate by a native groundwater microbial consortium. PeerJ 2019; 7:e6498. [PMID: 30941266 PMCID: PMC6440457 DOI: 10.7717/peerj.6498] [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: 12/30/2017] [Accepted: 01/20/2019] [Indexed: 02/01/2023] Open
Abstract
Gold ore processing typically generates large amounts of thiocyanate (SCN−)-contaminated effluent. When this effluent is stored in unlined tailings dams, contamination of the underlying aquifer can occur. The potential for bioremediation of SCN−-contaminated groundwater, either in situ or ex situ, remains largely unexplored. This study aimed to enrich and characterise SCN−-degrading microorganisms from mining-contaminated groundwater under a range of culturing conditions. Mildly acidic and suboxic groundwater, containing ∼135 mg L−1 SCN−, was collected from an aquifer below an unlined tailings dam. An SCN−-degrading consortium was enriched from contaminated groundwater using combinatory amendments of air, glucose and phosphate. Biodegradation occurred in all oxic cultures, except with the sole addition of glucose, but was inhibited by NH4+ and did not occur under anoxic conditions. The SCN−-degrading consortium was characterised using 16S and 18S rRNA gene sequencing, identifying a variety of heterotrophic taxa in addition to sulphur-oxidising bacteria. Interestingly, few recognised SCN−-degrading taxa were identified in significant abundance. These results provide both proof-of-concept and the required conditions for biostimulation of SCN− degradation in groundwater by native aquifer microorganisms.
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Affiliation(s)
- Liam P Spurr
- School of Earth Sciences, University of Melbourne, Parkville, Australia
| | - Mathew P Watts
- School of Earth Sciences, University of Melbourne, Parkville, Australia
| | - Han M Gan
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Australia
| | - John W Moreau
- School of Earth Sciences, University of Melbourne, Parkville, Australia
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19
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Ni G, Canizales S, Broman E, Simone D, Palwai VR, Lundin D, Lopez-Fernandez M, Sleutels T, Dopson M. Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells. Front Microbiol 2018; 9:2308. [PMID: 30323799 PMCID: PMC6172326 DOI: 10.3389/fmicb.2018.02308] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/10/2018] [Indexed: 11/25/2022] Open
Abstract
Thiocyanate is a toxic compound produced by the mining and metallurgy industries that needs to be remediated prior to its release into the environment. If the industry is situated at high altitudes or near the poles, economic factors require a low temperature treatment process. Microbial fuel cells are a developing technology that have the benefits of both removing such toxic compounds while recovering electrical energy. In this study, simultaneous thiocyanate degradation and electrical current generation was demonstrated and it was suggested that extracellular electron transfer to the anode occurred. Investigation of the microbial community by 16S rRNA metatranscriptome reads supported that the anode attached and planktonic anolyte consortia were dominated by a Thiobacillus-like population. Metatranscriptomic sequencing also suggested thiocyanate degradation primarily occurred via the ‘cyanate’ degradation pathway. The generated sulfide was metabolized via sulfite and ultimately to sulfate mediated by reverse dissimilatory sulfite reductase, APS reductase, and sulfate adenylyltransferase and the released electrons were potentially transferred to the anode via soluble electron shuttles. Finally, the ammonium from thiocyanate degradation was assimilated to glutamate as nitrogen source and carbon dioxide was fixed as carbon source. This study is one of the first to demonstrate a low temperature inorganic sulfur utilizing microbial fuel cell and the first to provide evidence for pathways of thiocyanate degradation coupled to electron transfer.
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Affiliation(s)
- Gaofeng Ni
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Sebastian Canizales
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Elias Broman
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Domenico Simone
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Viraja R Palwai
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Margarita Lopez-Fernandez
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Tom Sleutels
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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20
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Li D, Xie F, Zhang J. Voltammetric Behaviors and Determination of Thiocyanate on Multiwalled Carbon Nanotubes-Cetyltrimethylammonium Bromide Modified Electrode. ELECTROANAL 2018. [DOI: 10.1002/elan.201800422] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Dan Li
- School of Chemistry and Biological Engineering; Changsha University of Science and Technology; Changsha 410114 China
| | - Fangfang Xie
- School of Chemistry and Chemical Engineering; Huazhong University of Science and Technology; Wuhan 430074 China
| | - Jingdong Zhang
- School of Chemistry and Chemical Engineering; Huazhong University of Science and Technology; Wuhan 430074 China
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21
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Molecular insights into the activity and mechanism of cyanide hydratase enzyme associated with cyanide biodegradation by Serratia marcescens. Arch Microbiol 2018; 200:971-977. [DOI: 10.1007/s00203-018-1524-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/27/2018] [Accepted: 05/03/2018] [Indexed: 10/16/2022]
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22
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Deng Y, Li B, Zhang T. Bacteria That Make a Meal of Sulfonamide Antibiotics: Blind Spots and Emerging Opportunities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:3854-3868. [PMID: 29498514 DOI: 10.1021/acs.est.7b06026] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The release of sulfonamide antibiotics into the environment is alarming because the existence of these antibiotics in the environment may promote resistance in clinically relevant microorganisms, which is a potential threat to the effectiveness of antibiotic therapies. Controllable biodegradation processes are of particular significance for the inexpensive yet effective restoration of sulfonamide-contaminated environments. Cultivation-based techniques have already made great strides in successfully isolating bacteria with promising sulfonamide degradation abilities, but the implementation of these isolates in bioremediation has been limited by unknown microbial diversity, vast population responsiveness, and the impact of perturbations from open and complex environments. Advances in DNA sequencing technologies and metagenomic analyses are being used to complement the information derived from cultivation-based procedures. In this Review, we provide an overview of the growing understanding of isolated sulfonamide degraders and identify shortcomings of the prevalent literature in this field. In addition, we propose a technical paradigm that integrates experimental testing with metagenomic analysis to pave the way for improved understanding and exploitation of these ecologically important isolates. Overall, this Review aims to outline how metagenomic studies of isolated sulfonamide degraders are being applied for the advancement of bioremediation strategies for sulfonamide contamination.
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Affiliation(s)
- Yu Deng
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong , PR China
| | - Bing Li
- Division of Energy & Environment, Graduate School at Shenzhen , Tsinghua University , Shenzhen 518055 , PR China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong , PR China
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Deng Y, Wang Y, Mao Y, Zhang T. Partnership of Arthrobacter and Pimelobacter in Aerobic Degradation of Sulfadiazine Revealed by Metagenomics Analysis and Isolation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:2963-2972. [PMID: 29378398 DOI: 10.1021/acs.est.7b05913] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this study, metagenomic analyses were combined with cultivation-based techniques as a nested approach to identify functionally significant bacteria for sulfadiazine biodegradation within enrichment communities. The metagenomic investigations indicated that our previously isolated sulfadiazine degrader, Arthrobacter sp. D2, and another Pimelobacter bacterium concomitantly occurred as most abundant members in the community of an enrichment culture that performed complete sulfadiazine mineralization for over two years. Responses of the enriched populations to sole carbon source alternation further suggested the ability of this Pimelobacter member to grow on 2-aminopyrimidine, the most prominent intermediate metabolite of sulfadiazine. Taking advantage of this propensity, additional cultivation procedures have enabled the successful isolation of Pimelobacter sp. LG209, whose genomic sequences exactly matched that of the dominant Pimelobacter bacterium in the sulfadiazine enrichment culture. Integration of metagenomic investigations with the physiological characteristics of the isolates conclusively demonstrated that the sulfadiazine mineralization in a long-running enrichment culture was prominently mediated by primary sulfadiazine-degrading specialist strain Arthrobacter sp. D2 in association with the 2-aminopyrimidine-degrading partner strain Pimelobacter sp. LG209. Here, we provided the first mechanistic insight into microbial interactions in steady sulfadiazine mineralization processes, which will help develop appropriate bioremediation strategies for sulfadiazine-contaminated hotspot sites.
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Affiliation(s)
- Yu Deng
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong , China
| | - Yulin Wang
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong , China
| | - Yanping Mao
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong , China
- College of Chemistry and Environmental Engineering , Shenzhen University , Shenzhen , 518060 China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong , China
- International Center for Antibiotic Resistance in the Environment , Southern University of Science and Technology , Shenzhen , 518055 China
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24
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Castelle CJ, Banfield JF. Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life. Cell 2018. [DOI: 10.1016/j.cell.2018.02.016] [Citation(s) in RCA: 317] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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25
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Pan J, Wei C, Fu B, Ma J, Preis S, Wu H, Zhu S. Simultaneous nitrite and ammonium production in an autotrophic partial denitrification and ammonification of wastewaters containing thiocyanate. BIORESOURCE TECHNOLOGY 2018; 252:20-27. [PMID: 29306125 DOI: 10.1016/j.biortech.2017.12.059] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 12/17/2017] [Accepted: 12/18/2017] [Indexed: 06/07/2023]
Abstract
Various products are observed in biological oxidation and reduction of molecules containing elements of variable valence. The variability is caused by the diversity of microorganisms and their metabolic enzymes, which may develop into novel processes in wastewater treatment. The study aimed to develop a novel denitrification process forming nitrite and ammonium in wastewaters containing thiocyanate. High-efficiency nitrite and ammonium production was observed due to autotrophic partial denitrification and ammonification as a result of nitrate and thiocyanate removal. Nitrite, ammonium and sulfate were observed as the ultimate products. The increased NO3--N/SCN--N ratio in the treated wastewater resulted in the decreased removal efficiency of nitrate, and the increased nitrate-to-nitrite transformation ratio and the ratio of NO2--N to NH4+-N. Thiocyanate sulfur was oxidized to sulfate via intermediate elementary sulfur providing electron to nitrate or nitrite. The Thiobacillus genus dominated in the sludge providing ammonium and nitrite as substrate for the potentially anammox process.
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Affiliation(s)
- Jianxin Pan
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou 510006, PR China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou 510006, PR China
| | - Bingbing Fu
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou 510006, PR China
| | - Jingde Ma
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou 510006, PR China
| | - Sergei Preis
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou 510006, PR China
| | - Haizhen Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China.
| | - Shuang Zhu
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
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26
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West PT, Probst AJ, Grigoriev IV, Thomas BC, Banfield JF. Genome-reconstruction for eukaryotes from complex natural microbial communities. Genome Res 2018; 28:569-580. [PMID: 29496730 PMCID: PMC5880246 DOI: 10.1101/gr.228429.117] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 02/27/2018] [Indexed: 11/24/2022]
Abstract
Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k-mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities.
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Affiliation(s)
- Patrick T West
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Alexander J Probst
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA
| | - Igor V Grigoriev
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.,US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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27
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Liu M, Preis S, Kornev I, Hu Y, Wei CH. Pulsed corona discharge for improving treatability of coking wastewater. J Environ Sci (China) 2018; 64:306-316. [PMID: 29478652 DOI: 10.1016/j.jes.2017.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/03/2017] [Accepted: 07/04/2017] [Indexed: 06/08/2023]
Abstract
Coking wastewater (CW) contains toxic and macromolecular substances that inhibit biological treatment. The refractory compounds remaining in biologically treated coking wastewater (BTCW) provide chemical oxygen demand (COD) and color levels that make it unacceptable for reuse or disposal. Gas-phase pulsed corona discharge (PCD) utilizing mostly hydroxyl radicals and ozone as oxidants was applied to both raw coking wastewater (RCW) and BTCW wastewater as a supplemental treatment. The energy efficiency of COD, phenol, thiocyanate and cyanide degradation by PCD was the subject of the research. The cost-effective removal of intermediate oxidation products with addition of lime was also studied. The energy efficiency of oxidation was inversely proportional to the pulse repetition frequency: lower frequency allows more effective utilization of ozone at longer treatment times. Oxidative treatment of RCW showed the removal of phenol and thiocyanate at 800 pulses per second from 611 to 227mg/L and from 348 to 86mg/L, respectively, at 42kWh/m3 delivered energy, with substantial improvement in the BOD5/COD ratio (from 0.14 to 0.43). The COD and color of BTCW were removed by 30% and 93%, respectively, at 20kWh/m3, showing energy efficiency for the PCD treatment exceeding that of conventional ozonation by a factor of 3-4. Application of lime appeared to be an effective supplement to the PCD treatment of RCW, degrading COD by about 28% at an energy input of 28kWh/m3 and the lime dose of 3.0kg/m3. The improvement of RCW treatability is attributed to the degradation of toxic substances and fragmentation of macromolecular compounds.
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Affiliation(s)
- Ming Liu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Engineering and Technology Research Centre for Environmental Risk Prevention and Emergency Disposal, Guangzhou 510006, China.
| | - Sergei Preis
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China.
| | - Iakov Kornev
- Institute of High Technology Physics, National Research Tomsk Polytechnic University, 30 Lenin Ave., Tomsk 634050, Russian Federation
| | - Yun Hu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Engineering and Technology Research Centre for Environmental Risk Prevention and Emergency Disposal, Guangzhou 510006, China
| | - Chao-Hai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Engineering and Technology Research Centre for Environmental Risk Prevention and Emergency Disposal, Guangzhou 510006, China
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28
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Watts MP, Moreau JW. Thiocyanate biodegradation: harnessing microbial metabolism for mine remediation. MICROBIOLOGY AUSTRALIA 2018. [DOI: 10.1071/ma18047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Thiocyanate (SCN–) forms in the reaction between cyanide (CN–) and reduced sulfur species, e.g. in gold ore processing and coal-coking wastewater streams, where it is present at millimolar (mM) concentrations1. Thiocyanate is also present naturally at nM to µM concentrations in uncontaminated aquatic environments2. Although less toxic than its precursor CN–, SCN– can harm plants and animals at higher concentrations3, and thus needs to be removed from wastewater streams prior to disposal or reuse. Fortunately, SCN– can be biodegraded by microorganisms as a supply of reduced sulfur and nitrogen for energy sources, in addition to nutrients for growth4. Research into how we can best harness the ability of microbes to degrade SCN– may offer newer, more cost-effective and environmentally sustainable treatment solutions5. By studying biodegradation pathways of SCN– in laboratory and field treatment bioreactor systems, we can also gain fundamental insights into connections across the natural biogeochemical cycles of carbon, sulfur and nitrogen6.
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29
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Schulz F, Yutin N, Ivanova NN, Ortega DR, Lee TK, Vierheilig J, Daims H, Horn M, Wagner M, Jensen GJ, Kyrpides NC, Koonin EV, Woyke T. Giant viruses with an expanded complement of translation system components. Science 2017; 356:82-85. [PMID: 28386012 DOI: 10.1126/science.aal4657] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/18/2017] [Accepted: 03/15/2017] [Indexed: 12/24/2022]
Abstract
The discovery of giant viruses blurred the sharp division between viruses and cellular life. Giant virus genomes encode proteins considered as signatures of cellular organisms, particularly translation system components, prompting hypotheses that these viruses derived from a fourth domain of cellular life. Here we report the discovery of a group of giant viruses (Klosneuviruses) in metagenomic data. Compared with other giant viruses, the Klosneuviruses encode an expanded translation machinery, including aminoacyl transfer RNA synthetases with specificities for all 20 amino acids. Notwithstanding the prevalence of translation system components, comprehensive phylogenomic analysis of these genes indicates that Klosneuviruses did not evolve from a cellular ancestor but rather are derived from a much smaller virus through extensive gain of host genes.
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Affiliation(s)
- Frederik Schulz
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Natalia N Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Davi R Ortega
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Tae Kwon Lee
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, "Chemistry Meets Microbiology" Research Network, University of Vienna, 1090 Vienna, Austria
| | - Julia Vierheilig
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, "Chemistry Meets Microbiology" Research Network, University of Vienna, 1090 Vienna, Austria
| | - Holger Daims
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, "Chemistry Meets Microbiology" Research Network, University of Vienna, 1090 Vienna, Austria
| | - Matthias Horn
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, "Chemistry Meets Microbiology" Research Network, University of Vienna, 1090 Vienna, Austria
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, "Chemistry Meets Microbiology" Research Network, University of Vienna, 1090 Vienna, Austria
| | - Grant J Jensen
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
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30
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Luque-Almagro VM, Cabello P, Sáez LP, Olaya-Abril A, Moreno-Vivián C, Roldán MD. Exploring anaerobic environments for cyanide and cyano-derivatives microbial degradation. Appl Microbiol Biotechnol 2017; 102:1067-1074. [PMID: 29209795 PMCID: PMC5778177 DOI: 10.1007/s00253-017-8678-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/23/2017] [Accepted: 11/24/2017] [Indexed: 11/25/2022]
Abstract
Cyanide is one of the most toxic chemicals for living organisms described so far. Its toxicity is mainly based on the high affinity that cyanide presents toward metals, provoking inhibition of essential metalloenzymes. Cyanide and its cyano-derivatives are produced in a large scale by many industrial activities related to recovering of precious metals in mining and jewelry, coke production, steel hardening, synthesis of organic chemicals, and food processing industries. As consequence, cyanide-containing wastes are accumulated in the environment becoming a risk to human health and ecosystems. Cyanide and related compounds, like nitriles and thiocyanate, are degraded aerobically by numerous bacteria, and therefore, biodegradation has been offered as a clean and cheap strategy to deal with these industrial wastes. Anaerobic biological treatments are often preferred options for wastewater biodegradation. However, at present very little is known about anaerobic degradation of these hazardous compounds. This review is focused on microbial degradation of cyanide and related compounds under anaerobiosis, exploring their potential application in bioremediation of industrial cyanide-containing wastes.
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Affiliation(s)
- Víctor M Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - Purificación Cabello
- Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de Córdoba, Edificio Celestino Mutis, Campus de Rabanales, 14071, Córdoba, Spain
| | - Lara P Sáez
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain.
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31
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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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32
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van der Walt AJ, van Goethem MW, Ramond JB, Makhalanyane TP, Reva O, Cowan DA. Assembling metagenomes, one community at a time. BMC Genomics 2017; 18:521. [PMID: 28693474 PMCID: PMC5502489 DOI: 10.1186/s12864-017-3918-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/02/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Metagenomics allows unprecedented access to uncultured environmental microorganisms. The analysis of metagenomic sequences facilitates gene prediction and annotation, and enables the assembly of draft genomes, including uncultured members of a community. However, while several platforms have been developed for this critical step, there is currently no clear framework for the assembly of metagenomic sequence data. RESULTS To assist with selection of an appropriate metagenome assembler we evaluated the capabilities of nine prominent assembly tools on nine publicly-available environmental metagenomes, as well as three simulated datasets. Overall, we found that SPAdes provided the largest contigs and highest N50 values across 6 of the 9 environmental datasets, followed by MEGAHIT and metaSPAdes. MEGAHIT emerged as a computationally inexpensive alternative to SPAdes, assembling the most complex dataset using less than 500 GB of RAM and within 10 hours. CONCLUSIONS We found that assembler choice ultimately depends on the scientific question, the available resources and the bioinformatic competence of the researcher. We provide a concise workflow for the selection of the best assembly tool.
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Affiliation(s)
- Andries Johannes van der Walt
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa.,Centre for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria, Pretoria, South Africa
| | - Marc Warwick van Goethem
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa
| | - Thulani Peter Makhalanyane
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa
| | - Oleg Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria, Pretoria, South Africa
| | - Don Arthur Cowan
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa.
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