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Kumari S, Kumar A, Lepcha A, Kumar R. Cold-adapted Exiguobacterium sibiricum K1 as a potential bioinoculant in cold regions: Physiological and genomic elucidation of biocontrol and plant growth promotion. Gene 2024; 916:148439. [PMID: 38583819 DOI: 10.1016/j.gene.2024.148439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/22/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
The scarcity of soil nutrient availability under cold conditions of Himalayan regions needs a sustainable approach for better crop yields. The cold-adapted bacteria, Exiguobacterium sibiricum K1, with the potential to produce several plant growth-promoting (PGP) attributes, nitrogen fixation, indole acetic acid production, phosphate and potassium solubilization at 10 °C can provide an opportunity to promote crop yield improvement in an eco-friendly way under cold conditions. The bacterium also exhibited biocontrol activity against two phytopathogens and produced siderophore (53.0 ± 0.5 % psu). The strain's PGP properties were investigated using a spinach-based bioassay under controlled conditions. The bacterized seeds showed a notable increase in germination rate (23.2 %), shoot length (65.3 %), root length (56.6 %), leaf area (73.7 %), number of leaflets (65.2 %), and dry matter (65.2 %). Additionally, the leaf analysis indicated elevated chlorophyll pigments, i.e., chlorophyll a (55.5 %), chlorophyll b (42.8 %), carotenoids (35.2 %), percentage radical scavenging activity (47.4 %), and leaf nutrient uptake such as nitrogen (23.4 %), calcium (60.8 %), potassium (62.3 %), and magnesium (28.9 %). Moreover, the whole-genome sequencing and genome mining endorsed various biofertilisation-related genes, including genes for potassium and phosphate solubilization, iron and nitrogen acquisition, carbon dioxide fixation, and biocontrol ability of Exiguobacterium sibiricum K1. Overall, this study highlights the role of Exiguobacterium sibiricum K1 as a potential bioinoculant for improving crop yield under cold environments.
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Affiliation(s)
- Sareeka Kumari
- High Altitude Microbiology Laboratory (HAM-LAB), Biotechnology Division, CSIR -Institute of Himalayan and Bioresource Technology, Palampur, H.P. 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Anil Kumar
- High Altitude Microbiology Laboratory (HAM-LAB), Biotechnology Division, CSIR -Institute of Himalayan and Bioresource Technology, Palampur, H.P. 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Ayush Lepcha
- High Altitude Microbiology Laboratory (HAM-LAB), Biotechnology Division, CSIR -Institute of Himalayan and Bioresource Technology, Palampur, H.P. 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Rakshak Kumar
- High Altitude Microbiology Laboratory (HAM-LAB), Biotechnology Division, CSIR -Institute of Himalayan and Bioresource Technology, Palampur, H.P. 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India; Department of Molecular Biology & Bioinformatics, Tripura University (A Central University), Suryamaninagar, Tripura, 799022, India.
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2
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Nesbø CL, Fitamo TM, Lee H, Edwards EA. Metagenomes and metagenome-assembled genomes from a sequentially fed anaerobic digester treating solid organic municipal waste. Microbiol Resour Announc 2024; 13:e0091923. [PMID: 38126755 DOI: 10.1128/mra.00919-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
We present a data set of four metagenomes and 281 metagenome-assembled genomes describing the microbial community of a laboratory-scale high solids anaerobic digester. Our objective was to obtain information on the coding potential of the microbial community and draft genomes of the most abundant organisms in the digester.
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Affiliation(s)
- Camilla L Nesbø
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto, Ontario, Canada
- BioZone, University of Toronto , Toronto, Ontario, Canada
| | - Temesgen M Fitamo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto, Ontario, Canada
- BioZone, University of Toronto , Toronto, Ontario, Canada
| | - Hyunwoo Lee
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto, Ontario, Canada
- BioZone, University of Toronto , Toronto, Ontario, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto, Ontario, Canada
- BioZone, University of Toronto , Toronto, Ontario, Canada
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Kuroda K, Tomita S, Kurashita H, Hatamoto M, Yamaguchi T, Hori T, Aoyagi T, Sato Y, Inaba T, Habe H, Tamaki H, Hagihara Y, Tamura T, Narihiro T. Metabolic implications for predatory and parasitic bacterial lineages in activated sludge wastewater treatment systems. WATER RESEARCH X 2023; 20:100196. [PMID: 37662426 PMCID: PMC10469934 DOI: 10.1016/j.wroa.2023.100196] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/03/2023] [Accepted: 08/12/2023] [Indexed: 09/05/2023]
Abstract
Deciphering unclear microbial interactions is key to improving biological wastewater treatment processes. Microbial predation and parasitism in wastewater treatment ecosystems are unexplored survival strategies that have long been known and have recently attracted attention because these interspecies interactions may contribute to the reduction of excess sludge. Here, microbial community profiling of 600 activated sludge samples taken from six industrial and one municipal wastewater treatment processes (WWTPs) was conducted. To identify the shared lineages in the WWTPs, the shared microbial constituents were defined as the family level taxa that had ≥ 0.1% average relative abundance and detected in all processes. The microbial community analysis assigned 106 families as the shared microbial constituents in the WWTPs. Correlation analysis showed that 98 of the 106 shared families were significantly correlated with total carbon (TC) and/or total nitrogen (TN) concentrations, suggesting that they may contribute to wastewater remediation. Most possible predatory or parasitic bacteria belonging to the phyla Bdellovibrionota, Myxococcota, and Candidatus Patescibacteria were found to be the shared families and negatively correlated with TC/TN; thus, they were frequently present in the WWTPs and could be involved in the removal of carbon/nitrogen derived from cell components. Shotgun metagenome-resolved metabolic reconstructions indicated that gene homologs associated with predation or parasitism are conserved in the Bdellovibrionota, Myxococcota, and Ca. Patescibacteria genomes (e.g., host interaction (hit) locus, Tad-like secretion complexes, and type IV pilus assembly proteins). This study provides insights into the complex microbial interactions potentially linked to the reduction of excess sludge biomass in these processes.
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Affiliation(s)
- Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2‐17‐2‐1 Tsukisamu‐Higashi, Toyohira‐Ku, Sapporo, Hokkaido 062‐8517 Japan
| | - Shun Tomita
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2‐17‐2‐1 Tsukisamu‐Higashi, Toyohira‐Ku, Sapporo, Hokkaido 062‐8517 Japan
| | - Hazuki Kurashita
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2‐17‐2‐1 Tsukisamu‐Higashi, Toyohira‐Ku, Sapporo, Hokkaido 062‐8517 Japan
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka-Machi, Nagaoka, Niigata 940-2188 Japan
| | - Masashi Hatamoto
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka-Machi, Nagaoka, Niigata 940-2188 Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka-Machi, Nagaoka, Niigata 940-2188 Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki 305–8569, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki 305–8569, Japan
| | - Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki 305–8569, Japan
| | - Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki 305–8569, Japan
| | - Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki 305–8569, Japan
| | - Hideyuki Tamaki
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Yoshihisa Hagihara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Tomohiro Tamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2‐17‐2‐1 Tsukisamu‐Higashi, Toyohira‐Ku, Sapporo, Hokkaido 062‐8517 Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2‐17‐2‐1 Tsukisamu‐Higashi, Toyohira‐Ku, Sapporo, Hokkaido 062‐8517 Japan
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Xiao Y, Chen L, Teng K, Ma J, Xiang S, Jiang L, Liu G, Yang B, Fang J. Potential roles of the rhizospheric bacterial community in assisting Miscanthus floridulus in remediating multi-metal(loid)s contaminated soils. ENVIRONMENTAL RESEARCH 2023; 227:115749. [PMID: 36965787 DOI: 10.1016/j.envres.2023.115749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/23/2023] [Accepted: 03/22/2023] [Indexed: 05/08/2023]
Abstract
Phytoremediation technology is an important approach applied to heavy metal remediation, and how to improve its remediation efficiency is the key. In this study, we compared the rhizospheric bacterial communities and metals contents in Miscanthus floridulus (M. floridulus) of four towns, including Huayuan Town (HY), Longtan Town (LT), Maoer Village (ME), and Minle Town (ML) around the lead-zinc mining area in Huayuan County, China. The roles of rhizospheric bacterial communities in assisting the phytoremediation of M. floridulus were explored. It was found that the compositions of the rhizospheric bacterial community of M. floridulus differed in four regions, but majority of them were heavy metal-resistant bacteria that could promote plant growth. Results of bioconcentration factors showed the enrichment of Cu, Zn, and Pb by M. floridulus in these four regions were significantly different. The Zn enrichment capacity of ML was the strongest for Cu and stronger than LT and ME for Pb. The enrichment capacity of LT and ML was stronger than HY and ME. These bacteria may influence the different heavy metals uptake of M. floridulus by altering the soil physiochemical properties (e.g., soil peroxidase, pH and moisture content). In addition, co-occurrence network analysis also showed that LT and ML had higher network stability and complexity than HY and ME. Functional prediction analysis of the rhizospheric bacterial community showed that genes related to protein synthesis (e.g., zinc-binding alcohol dehydrogenase/oxidoreductase, Dtx R family transcriptional regulators and ACC deaminase) also contributed to phytoremediation in various ways. This study provides theoretical guidance for selecting suitable microorganisms to assist in the phytoremediation of heavy metals.
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Affiliation(s)
- Yunhua Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Liang Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Kai Teng
- Hunan Tobacco Science Institute, Changsha, 410004, China
| | - Jingjing Ma
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Sha Xiang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Lihong Jiang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Gang Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Bo Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
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Botté ES, Bennett H, Engelberts JP, Thomas T, Bell JJ, Webster NS, Luter HM. Future ocean conditions induce necrosis, microbial dysbiosis and nutrient cycling imbalance in the reef sponge Stylissa flabelliformis. ISME COMMUNICATIONS 2023; 3:53. [PMID: 37311801 PMCID: PMC10264452 DOI: 10.1038/s43705-023-00247-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/22/2023] [Accepted: 04/14/2023] [Indexed: 06/15/2023]
Abstract
Oceans are rapidly warming and acidifying in the context of climate change, threatening sensitive marine biota including coral reef sponges. Ocean warming (OW) and ocean acidification (OA) can impact host health and associated microbiome, but few studies have investigated these effects, which are generally studied in isolation, on a specific component of the holobiont. Here we present a comprehensive view of the consequences of simultaneous OW and OA for the tropical sponge Stylissa flabelliformis. We found no interactive effect on the host health or microbiome. Furthermore, OA (pH 7.6 versus pH 8.0) had no impact, while OW (31.5 °C versus 28.5 °C) caused tissue necrosis, as well as dysbiosis and shifts in microbial functions in healthy tissue of necrotic sponges. Major taxonomic shifts included a complete loss of archaea, reduced proportions of Gammaproteobacteria and elevated relative abundances of Alphaproteobacteria. OW weakened sponge-microbe interactions, with a reduced capacity for nutrient exchange and phagocytosis evasion, indicating lower representations of stable symbionts. The potential for microbially-driven nitrogen and sulphur cycling was reduced, as was amino acid metabolism. Crucially, the dysbiosis annihilated the potential for ammonia detoxification, possibly leading to accumulation of toxic ammonia, nutrient imbalance, and host tissue necrosis. Putative defence against reactive oxygen species was greater at 31.5 °C, perhaps as microorganisms capable of resisting temperature-driven oxidative stress were favoured. We conclude that healthy symbiosis in S. flabelliformis is unlikely to be disrupted by future OA but will be deeply impacted by temperatures predicted for 2100 under a "business-as-usual" carbon emission scenario.
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Affiliation(s)
- Emmanuelle S Botté
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
- Australian Institute of Marine Science, Townsville, Queensland, Australia.
| | - Holly Bennett
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- Victoria University of Wellington, Wellington, New Zealand
- Cawthron Institute, Nelson, New Zealand
| | - J Pamela Engelberts
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - James J Bell
- Victoria University of Wellington, Wellington, New Zealand
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- Australian Antarctic Division, Hobart, Tasmania, Australia
| | - Heidi M Luter
- Australian Institute of Marine Science, Townsville, Queensland, Australia.
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Nam NN, Do HDK, Loan Trinh KT, Lee NY. Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions. Foods 2023; 12:foods12112140. [PMID: 37297385 DOI: 10.3390/foods12112140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.
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Affiliation(s)
- Nguyen Nhat Nam
- Biotechnology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 72820, Vietnam
| | - Kieu The Loan Trinh
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
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Mukhia S, Kumar A, Kumar R. Antioxidant prodigiosin-producing cold-adapted Janthinobacterium sp. ERMR3:09 from a glacier moraine: Genomic elucidation of cold adaptation and pigment biosynthesis. Gene X 2023; 857:147178. [PMID: 36627092 DOI: 10.1016/j.gene.2023.147178] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/17/2022] [Accepted: 01/04/2023] [Indexed: 01/08/2023] Open
Abstract
Janthinobacterium from cold niches has been studied broadly for bioactive violacein production. However, reports on the atypical red-pigmented Janthinobacterium strains are shallow. The bioactive red prodigiosin pigment has immense pharmacological significance, including antioxidant, antimicrobial and anticancer potential. Here, we report the first complete genome of a prodigiosin-producing Janthinobacterium sp. ERMR3:09 from Sikkim Himalaya in an attempt to elucidate its cold adaptation and prodigiosin biosynthesis. Nanopore sequencing and Flye assembly of the ERMR3:09 genome resulted in a single contig of 6,262,330 bp size and 62.26% GC content. Phylogenomic analysis and genome indices indicate that ERMR3:09 is a potentially novel species of the genus Janthinobacterium. The multicopy cold-responsive genes and gene upregulation under cold stress denoted its cold adaptation mechanisms. Genome analysis identified the unique genes, gene cluster and pathway for prodigiosin biosynthesis in ERMR3:09. Considering the notable antioxidant activity, it can be the next powerhouse of bioactive prodigiosin production.
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Affiliation(s)
- Srijana Mukhia
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur-176061, Himachal Pradesh, India; Department of Microbiology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Anil Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur-176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Rakshak Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur-176061, Himachal Pradesh, India.
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Sarton-Lohéac G, Nunes da Silva CG, Mazel F, Baud G, de Bakker V, Das S, El Chazli Y, Ellegaard K, Garcia-Garcera M, Glover N, Liberti J, Nacif Marçal L, Prasad A, Somerville V, Bonilla-Rosso G, Engel P. Deep Divergence and Genomic Diversification of Gut Symbionts of Neotropical Stingless Bees. mBio 2023; 14:e0353822. [PMID: 36939321 PMCID: PMC10128065 DOI: 10.1128/mbio.03538-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
Social bees harbor conserved gut microbiotas that may have been acquired in a common ancestor of social bees and subsequently codiversified with their hosts. However, most of this knowledge is based on studies on the gut microbiotas of honey bees and bumblebees. Much less is known about the gut microbiotas of the third and most diverse group of social bees, the stingless bees. Specifically, the absence of genomic data from their microbiotas presents an important knowledge gap in understanding the evolution and functional diversity of the social bee microbiota. Here, we combined community profiling with culturing and genome sequencing of gut bacteria from six neotropical stingless bee species from Brazil. Phylogenomic analyses show that most stingless bee gut isolates form deep-branching sister clades of core members of the honey bee and bumblebee gut microbiota with conserved functional capabilities, confirming the common ancestry and ecology of their microbiota. However, our bacterial phylogenies were not congruent with those of the host, indicating that the evolution of the social bee gut microbiota was not driven by strict codiversification but included host switches and independent symbiont gain and losses. Finally, as reported for the honey bee and bumblebee microbiotas, we found substantial genomic divergence among strains of stingless bee gut bacteria, suggesting adaptation to different host species and glycan niches. Our study offers first insights into the genomic diversity of the stingless bee microbiota and highlights the need for broader samplings to understand the evolution of the social bee gut microbiota. IMPORTANCE Stingless bees are the most diverse group of the corbiculate bees and represent important pollinator species throughout the tropics and subtropics. They harbor specialized microbial communities in their gut that are related to those found in honey bees and bumblebees and that are likely important for bee health. Few bacteria have been cultured from the gut of stingless bees, which has prevented characterization of their genomic diversity and functional potential. Here, we established cultures of major members of the gut microbiotas of six stingless bee species and sequenced their genomes. We found that most stingless bee isolates belong to novel bacterial species distantly related to those found in honey bees and bumblebees and encoding similar functional capabilities. Our study offers a new perspective on the evolution of the social bee gut microbiota and presents a basis for characterizing the symbiotic relationships between gut bacteria and stingless bees.
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Affiliation(s)
- Garance Sarton-Lohéac
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Gilles Baud
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Vincent de Bakker
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sudip Das
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Yassine El Chazli
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Kirsten Ellegaard
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Natasha Glover
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joanito Liberti
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Lorena Nacif Marçal
- Department of Morphology, Instituto de Ciências Biológicas, Federal University of Amazonas, Manaus, Brazil
| | - Aiswarya Prasad
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Germán Bonilla-Rosso
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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Xu Z, Park TJ, Cao H. Advances in mining and expressing microbial biosynthetic gene clusters. Crit Rev Microbiol 2023; 49:18-37. [PMID: 35166616 DOI: 10.1080/1040841x.2022.2036099] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Natural products (NPs) especially the secondary metabolites originated from microbes exhibit great importance in biomedical, industrial and agricultural applications. However, mining biosynthetic gene clusters (BGCs) to produce novel NPs has been hindered owing that a large population of environmental microbes are unculturable. In the past decade, strategies to explore BGCs directly from (meta)genomes have been established along with the fast development of high-throughput sequencing technologies and the powerful bioinformatics data-processing tools, which greatly expedited the exploitations of novel BGCs from unculturable microbes including the extremophilic microbes. In this review, we firstly summarized the popular bioinformatics tools and databases available to mine novel BGCs from (meta)genomes based on either pure cultures or pristine environmental samples. Noticeably, approaches rooted from machine learning and deep learning with focuses on the prediction of ribosomally synthesized and post-translationally modified peptides (RiPPs) were dramatically increased in recent years. Moreover, synthetic biology techniques to express the novel BGCs in culturable native microbes or heterologous hosts were introduced. This working pipeline including the discovery and biosynthesis of novel NPs will greatly advance the exploitations of the abundant but unexplored microbial BGCs.
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Affiliation(s)
- Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Tae-Jin Park
- HME Healthcare Co., Ltd, Suwon-si, Republic of Korea
| | - Huiluo Cao
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
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Xiao Y, Chen L, Li C, Ma J, Chen R, Yang B, Liu G, Liu S, Fang J. Role of the rhizosphere bacterial community in assisting phytoremediation in a lead-zinc area. FRONTIERS IN PLANT SCIENCE 2023; 13:1106985. [PMID: 36874912 PMCID: PMC9982732 DOI: 10.3389/fpls.2022.1106985] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Heavy metals (HMs) contamination and vegetation destruction in the mining area caused by mining activities are severely increasing. It is urgent to restore vegetation and stabilize HMs. In this study, we compared the ability of HMs phytoextraction/phytostabilization of three dominant plants, including Artemisia argyi (LA), Miscanthus floridulus (LM), and Boehmeria nivea (LZ) in a lead-zinc mining area in Huayuan County (China). We also explored the role of the rhizosphere bacterial community in assisting phytoremediation using 16S rRNA sequencing technology. Bioconcentration factor (BCF) and translocation factor (TF) analysis showed that LA preferred accumulating Cd, LZ preferred accumulating Cr and Sb, and LM preferred accumulating Cr and Ni. Significant (p < 0.05) differences were found among the rhizosphere soil microbial communities of these three plants. The key genera of LA were Truepera and Anderseniella, that of LM were Paracoccus and Erythrobacter, and of LZ was Novosphingobium. Correlation analysis showed some rhizosphere bacterial taxa (e.g., Actinomarinicola, Bacillariophyta and Oscillochloris) affected some soil physicochemical parameters (e.g., organic matter and pH) of the rhizosphere soil and enhanced the TF of metals. Functional prediction analysis of soil bacterial community showed that the relative abundances of genes related to the synthesis of some proteins (e.g., manganese/zinc-transporting P-type ATPase C, nickel transport protein and 1-aminocyclopropane-1-carboxylate deaminase) was positively correlated with the phytoextraction/phytostabilization capacity of plants for heavy metals. This study provided theoretical guidance on selecting appropriate plants for different metal remediation applications. We also found some rhizosphere bacteria might enhance the phytoremediation of multi-metals, which could provide a reference for subsequent research.
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Affiliation(s)
- Yunhua Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Liang Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Chunxiao Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jingjing Ma
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Rui Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Bo Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Gang Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Shuming Liu
- College of Chemical and Environmental Sciences, YiLi Normal University, YiLi, China
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
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11
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A Review of Basic Bioinformatic Techniques for Microbial Community Analysis in an Anaerobic Digester. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Biogas production involves various types of intricate microbial populations in an anaerobic digester (AD). To understand the anaerobic digestion system better, a broad-based study must be conducted on the microbial population. Deep understanding of the complete metagenomics including microbial structure, functional gene form, similarity/differences, and relationships between metabolic pathways and product formation, could aid in optimization and enhancement of AD processes. With advancements in technologies for metagenomic sequencing, for example, next generation sequencing and high-throughput sequencing, have revolutionized the study of microbial dynamics in anaerobic digestion. This review includes a brief introduction to the basic process of metagenomics research and includes a detailed summary of the various bioinformatics approaches, viz., total investigation of data obtained from microbial communities using bioinformatics methods to expose metagenomics characterization. This includes (1) methods of DNA isolation and sequencing, (2) investigation of anaerobic microbial communities using bioinformatics techniques, (3) application of the analysis of anaerobic microbial community and biogas production, and (4) restriction and prediction of bioinformatics analysis on microbial metagenomics. The review has been concluded, giving a summarized insight into bioinformatic tools and also promoting the future prospects of integrating humungous data with artificial intelligence and neural network software.
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12
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Bhattacharya S, Roche R, Shuvo MH, Moussad B, Bhattacharya D. Contact-Assisted Threading in Low-Homology Protein Modeling. Methods Mol Biol 2023; 2627:41-59. [PMID: 36959441 DOI: 10.1007/978-1-0716-2974-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The ability to successfully predict the three-dimensional structure of a protein from its amino acid sequence has made considerable progress in the recent past. The progress is propelled by the improved accuracy of deep learning-based inter-residue contact map predictors coupled with the rising growth of protein sequence databases. Contact map encodes interatomic interaction information that can be exploited for highly accurate prediction of protein structures via contact map threading even for the query proteins that are not amenable to direct homology modeling. As such, contact-assisted threading has garnered considerable research effort. In this chapter, we provide an overview of existing contact-assisted threading methods while highlighting the recent advances and discussing some of the current limitations and future prospects in the application of contact-assisted threading for improving the accuracy of low-homology protein modeling.
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Affiliation(s)
- Sutanu Bhattacharya
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA
| | | | - Md Hossain Shuvo
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Bernard Moussad
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
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13
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Singh A, Ambaru B, Bandsode V, Ahmed N. Panomics to decode virulence and fitness in Gram-negative bacteria. Front Cell Infect Microbiol 2022; 12:1061596. [PMID: 36478674 PMCID: PMC9719987 DOI: 10.3389/fcimb.2022.1061596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/26/2022] [Indexed: 11/22/2022] Open
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14
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Navgire GS, Goel N, Sawhney G, Sharma M, Kaushik P, Mohanta YK, Mohanta TK, Al-Harrasi A. Analysis and Interpretation of metagenomics data: an approach. Biol Proced Online 2022; 24:18. [PMID: 36402995 PMCID: PMC9675974 DOI: 10.1186/s12575-022-00179-7] [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: 07/28/2022] [Accepted: 10/19/2022] [Indexed: 11/20/2022] Open
Abstract
Advances in next-generation sequencing technologies have accelerated the momentum of metagenomic studies, which is increasing yearly. The metagenomics field is one of the versatile applications in microbiology, where any interaction in the environment involving microorganisms can be the topic of study. Due to this versatility, the number of applications of this omics technology reached its horizons. Agriculture is a crucial sector involving crop plants and microorganisms interacting together. Hence, studying these interactions through the lenses of metagenomics would completely disclose a new meaning to crop health and development. The rhizosphere is an essential reservoir of the microbial community for agricultural soil. Hence, we focus on the R&D of metagenomic studies on the rhizosphere of crops such as rice, wheat, legumes, chickpea, and sorghum. These recent developments are impossible without the continuous advancement seen in the next-generation sequencing platforms; thus, a brief introduction and analysis of the available sequencing platforms are presented here to have a clear picture of the workflow. Concluding the topic is the discussion about different pipelines applied to analyze data produced by sequencing techniques and have a significant role in interpreting the outcome of a particular experiment. A plethora of different software and tools are incorporated in the automated pipelines or individually available to perform manual metagenomic analysis. Here we describe 8-10 advanced, efficient pipelines used for analysis that explain their respective workflows to simplify the whole analysis process.
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Affiliation(s)
- Gauri S Navgire
- Department of Microbiology, Savitribai Phule Pune University, Pune, Maharastra, 411007, India
| | - Neha Goel
- Department of Genetics and Tree Improvement, Forest Research Institute, 248006, Dehradun, India
| | - Gifty Sawhney
- Inflammation Pharmacology Division, Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Jammu-180001, Jammu Kashmir, India
| | - Mohit Sharma
- Department of Molecular Medicine, Medical University of Warsaw and Malopolska Center of Biotechnology, Karkow, Poland
| | | | | | - Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, 616, Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, 616, Oman.
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15
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Lobanov V, Gobet A, Joyce A. Ecosystem-specific microbiota and microbiome databases in the era of big data. ENVIRONMENTAL MICROBIOME 2022; 17:37. [PMID: 35842686 PMCID: PMC9287977 DOI: 10.1186/s40793-022-00433-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/29/2022] [Indexed: 05/05/2023]
Abstract
The rapid development of sequencing methods over the past decades has accelerated both the potential scope and depth of microbiota and microbiome studies. Recent developments in the field have been marked by an expansion away from purely categorical studies towards a greater investigation of community functionality. As in-depth genomic and environmental coverage is often distributed unequally across major taxa and ecosystems, it can be difficult to identify or substantiate relationships within microbial communities. Generic databases containing datasets from diverse ecosystems have opened a new era of data accessibility despite costs in terms of data quality and heterogeneity. This challenge is readily embodied in the integration of meta-omics data alongside habitat-specific standards which help contextualise datasets both in terms of sample processing and background within the ecosystem. A special case of large genomic repositories, ecosystem-specific databases (ES-DB's), have emerged to consolidate and better standardise sample processing and analysis protocols around individual ecosystems under study, allowing independent studies to produce comparable datasets. Here, we provide a comprehensive review of this emerging tool for microbial community analysis in relation to current trends in the field. We focus on the factors leading to the formation of ES-DB's, their comparison to traditional microbial databases, the potential for ES-DB integration with meta-omics platforms, as well as inherent limitations in the applicability of ES-DB's.
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Affiliation(s)
- Victor Lobanov
- Department of Marine Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden
| | | | - Alyssa Joyce
- Department of Marine Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden.
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16
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Tyx RE, Rivera AJ, Stanfill SB, Zaatari GS, Watson CH. Shotgun metagenome sequencing of a Sudanese toombak snuff tobacco: genetic attributes of a high tobacco-specific nitrosamine containing smokeless tobacco product. Lett Appl Microbiol 2022; 74:444-451. [PMID: 34862647 PMCID: PMC9204801 DOI: 10.1111/lam.13623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 11/28/2022]
Abstract
The most alarming aspect of the Sudanese toombak smokeless tobacco is that it contains high levels of highly toxic tobacco-specific nitrosamines (TSNAs). Understanding the microbiology of toombak is of relevance because TSNAs are an indirect result of microbial-mediated nitrate reductions. We conducted shotgun metagenomic sequencing on a toombak product for which relevant features are presented here. The microbiota was composed of over 99% Bacteria. The most abundant taxa included Actinobacteria, specifically the genera Enteractinococcus and Corynebacterium, while Firmicutes were represented by the family Bacillaceae and the genus Staphylococcus. Selected gene targets were nitrate reduction and transport, antimicrobial resistance, and other genetic transference mechanisms. Canonical nitrate reduction and transport genes (i.e. nar) were found for Enteractinococcus and Corynebacterium while various species of Staphylococcus exhibited a notable number of antimicrobial resistance and genetic transference genes. The nitrate reduction activity of the microbiota in toombak is suspected to be a contributing factor to its high levels of TSNAs. Additionally, the presence of antimicrobial resistance and transference genes could contribute to deleterious effects on oral and gastrointestinal health of the end user. Overall, the high toxicity and increased incidences of cancer and oral disease of toombak users warrants further investigation into the microbiology of toombak.
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Affiliation(s)
- R E Tyx
- Division of Laboratory Sciences at the Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - A J Rivera
- Division of Laboratory Sciences at the Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - S B Stanfill
- Division of Laboratory Sciences at the Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - G S Zaatari
- Department of Pathology and Laboratory Medicine, American University of Beirut, Beirut, Lebanon
| | - C H Watson
- Division of Laboratory Sciences at the Centers for Disease Control and Prevention, Atlanta, GA, USA
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17
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Ke J, Zhao Z, Coates CR, Hadjithomas M, Kuftin A, Louie K, Weller D, Thomashow L, Mouncey NJ, Northen TR, Yoshikuni Y. Development of platforms for functional characterization and production of phenazines using a multi-chassis approach via CRAGE. Metab Eng 2021; 69:188-197. [PMID: 34890798 DOI: 10.1016/j.ymben.2021.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 02/08/2023]
Abstract
Phenazines (Phzs), a family of chemicals with a phenazine backbone, are secondary metabolites with diverse properties such as antibacterial, anti-fungal, or anticancer activity. The core derivatives of phenazine, phenazine-1-carboxylic acid (PCA) and phenazine-1,6-dicarboxylic acid (PDC), are themselves precursors for various other derivatives. Recent advances in genome mining tools have enabled researchers to identify many biosynthetic gene clusters (BGCs) that might produce novel Phzs. To characterize the function of these BGCs efficiently, we performed modular construct assembly and subsequent multi-chassis heterologous expression using chassis-independent recombinase-assisted genome engineering (CRAGE). CRAGE allowed rapid integration of a PCA BGC into 23 diverse γ-proteobacteria species and allowed us to identify top PCA producers. We then used the top five chassis hosts to express four partially refactored PDC BGCs. A few of these platforms produced high levels of PDC. Specifically, Xenorhabdus doucetiae and Pseudomonas simiae produced PDC at a titer of 293 mg/L and 373 mg/L, respectively, in minimal media. These titers are significantly higher than those previously reported. Furthermore, selectivity toward PDC production over PCA production was improved by up to 9-fold. The results show that these strains are promising chassis for production of PCA, PDC, and their derivatives, as well as for function characterization of Phz BGCs identified via bioinformatics mining.
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Affiliation(s)
- Jing Ke
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zhiying Zhao
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cameron R Coates
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michalis Hadjithomas
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrea Kuftin
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katherine Louie
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Weller
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality, Washington State University, Pullman, WA, USA; Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Linda Thomashow
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality, Washington State University, Pullman, WA, USA; Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Nigel J Mouncey
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Trent R Northen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Global Center for Food, Land, and Water Resources, Hokkaido University, Hokkaido, 060-8589, Japan.
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18
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Kuroda K, Narihiro T, Nobu MK, Tobo A, Yamauchi M, Yamada M. Ecogenomics Reveals Microbial Metabolic Networks in a Psychrophilic Methanogenic Bioreactor Treating Soy Sauce Production Wastewater. Microbes Environ 2021; 36. [PMID: 34588388 PMCID: PMC8674449 DOI: 10.1264/jsme2.me21045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An ecogenomic analysis of the methanogenic microbial community in a laboratory-scale up-flow anaerobic sludge blanket (UASB) reactor treating soy sauce-processing wastewater revealed a synergistic metabolic network. Granular sludge samples were collected from the UASB reactor operated under psychrophilic (20°C) conditions with a COD removal rate >75%. A 16S rRNA gene amplicon sequencing-based microbial community analysis classified the major microbial taxa as Methanothrix, Methanobacterium, Pelotomaculaceae, Syntrophomonadaceae, Solidesulfovibrio, and members of the phyla Synergistota and Bacteroidota. Draft genomes of dominant microbial populations were recovered by metagenomic shotgun sequencing. Metagenomic- and metatranscriptomic-assisted metabolic reconstructions indicated that Synergistota- and Bacteroidota-related organisms play major roles in the degradation of amino acids. A metagenomic bin of the uncultured Bacteroidales 4484-276 clade encodes genes for proteins that may function in the catabolism of phenylalanine and tyrosine under microaerobic conditions. Syntrophomonadaceae and Pelotomaculaceae oxidize fatty acid byproducts presumably derived from the degradation of amino acids in syntrophic association with aceticlastic and hydrogenotrophic methanogen populations. Solidesulfovibrio organisms are responsible for the reduction of sulfite and may support the activity of hydrogenotrophic methanogens and other microbial populations by providing hydrogen and ammonia using nitrogen fixation-related proteins. Overall, functionally diverse anaerobic organisms unite to form a metabolic network that performs the complete degradation of amino acids in the psychrophilic methanogenic microbiota.
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Affiliation(s)
- Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Atsushi Tobo
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College
| | - Masahito Yamauchi
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College
| | - Masayoshi Yamada
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College
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19
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Haverkamp THA, Lossouarn J, Zhaxybayeva O, Lyu J, Bienvenu N, Geslin C, Nesbø CL. Newly identified proviruses in Thermotogota suggest that viruses are the vehicles on the highways of interphylum gene sharing. Environ Microbiol 2021; 23:7105-7120. [PMID: 34398506 DOI: 10.1111/1462-2920.15723] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/24/2021] [Accepted: 08/13/2021] [Indexed: 11/30/2022]
Abstract
Phylogenomic analyses of bacteria from the phylum Thermotogota have shown extensive lateral gene transfer with distantly related organisms, particularly with Firmicutes. One likely mechanism of such DNA transfer is viruses. However, to date, only three temperate viruses have been characterized in this phylum, all infecting bacteria from the Marinitoga genus. Here we report 17 proviruses integrated into genomes of bacteria belonging to eight Thermotogota genera and induce viral particle production from one of the proviruses. All except an incomplete provirus from Mesotoga fall into two groups based on sequence similarity, gene synteny and taxonomic classification. Proviruses of Group 1 are found in the genera Geotoga, Kosmotoga, Marinitoga, Thermosipho and Mesoaciditoga and are similar to the previously characterized Marinitoga viruses, while proviruses from Group 2 are distantly related to the Group 1 proviruses, have different genome organization and are found in Petrotoga and Defluviitoga. Genes carried by both groups are closely related to Firmicutes and Firmicutes (pro)viruses in phylogenetic analyses. Moreover, one of the groups show evidence of recent gene exchange and may be capable of infecting cells from both phyla. We hypothesize that viruses are responsible for a large portion of the observed gene flow between Firmicutes and Thermotogota.
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Affiliation(s)
- Thomas H A Haverkamp
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Julien Lossouarn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, 78350, France
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Jie Lyu
- Université Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, F-29280, France
| | - Nadège Bienvenu
- Université Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, F-29280, France
| | - Claire Geslin
- Université Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, F-29280, France
| | - Camilla L Nesbø
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
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20
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Kieft K, Breister AM, Huss P, Linz AM, Zanetakos E, Zhou Z, Rahlff J, Esser SP, Probst AJ, Raman S, Roux S, Anantharaman K. Virus-associated organosulfur metabolism in human and environmental systems. Cell Rep 2021; 36:109471. [PMID: 34348151 DOI: 10.1016/j.celrep.2021.109471] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 01/07/2021] [Accepted: 07/09/2021] [Indexed: 01/02/2023] Open
Abstract
Viruses influence the fate of nutrients and human health by killing microorganisms and altering metabolic processes. Organosulfur metabolism and biologically derived hydrogen sulfide play dynamic roles in manifestation of diseases, infrastructure degradation, and essential biological processes. Although microbial organosulfur metabolism is well studied, the role of viruses in organosulfur metabolism is unknown. Here, we report the discovery of 39 gene families involved in organosulfur metabolism encoded by 3,749 viruses from diverse ecosystems, including human microbiomes. The viruses infect organisms from all three domains of life. Six gene families encode for enzymes that degrade organosulfur compounds into sulfide, whereas others manipulate organosulfur compounds and may influence sulfide production. We show that viral metabolic genes encode key enzymatic domains, are translated into protein, and are maintained after recombination, and sulfide provides a fitness advantage to viruses. Our results reveal viruses as drivers of organosulfur metabolism with important implications for human and environmental health.
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Affiliation(s)
- Kristopher Kieft
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Adam M Breister
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Phil Huss
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexandra M Linz
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth Zanetakos
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Janina Rahlff
- Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Sarah P Esser
- Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Srivatsan Raman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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21
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Jensen S, Frank JA, Arntzen MØ, Duperron S, Vaaje-Kolstad G, Hovland M. Endozoicomonadaceae symbiont in gills of Acesta clam encodes genes for essential nutrients and polysaccharide degradation. FEMS Microbiol Ecol 2021; 97:6275716. [PMID: 33988698 PMCID: PMC8755941 DOI: 10.1093/femsec/fiab070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 05/12/2021] [Indexed: 01/29/2023] Open
Abstract
Gammaproteobacteria from the family Endozoicomonadaceae have emerged as widespread associates of dense marine animal communities. Their abundance in coral reefs involves symbiotic relationships and possibly host nutrition. We explored functions encoded in the genome of an uncultured Endozoicomonadaceae 'Candidatus Acestibacter aggregatus' that lives inside gill cells of large Acesta excavata clams in deep-water coral reefs off mid-Norway. The dominance and deep branching lineage of this symbiont was confirmed using 16S rRNA gene sequencing and phylogenomic analysis from shotgun sequencing data. The 4.5 Mb genome binned in this study has a low GC content of 35% and is enriched in transposon and chaperone gene annotations indicating ongoing adaptation. Genes encoding functions potentially involved with the symbiosis include ankyrins, repeat in toxins, secretion and nutritional systems. Complete pathways were identified for the synthesis of eleven amino acids and six B-vitamins. A minimal chitinolytic machinery was indicated from a glycosyl hydrolase GH18 and a lytic polysaccharide monooxygenase LPMO10. Expression of the latter was confirmed using proteomics. Signal peptides for secretion were identified for six polysaccharide degrading enzymes, ten proteases and three lipases. Our results suggest a nutritional symbiosis fuelled by enzymatic products from extracellular degradation processes.
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Affiliation(s)
- Sigmund Jensen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1432 Ås, Norway
| | - Jeremy A Frank
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1432 Ås, Norway
| | - Magnus Ø Arntzen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1432 Ås, Norway
| | - Sébastien Duperron
- UMR 7245 Muséum National d'Histoire Naturelle/CNRS Molécules de Communication et Adaptation des Micro-organismes and Institut Universitaire de France, CP39, 12 rue Buffon, F-75231 Paris Cedex 05, France
| | - Gustav Vaaje-Kolstad
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1432 Ås, Norway
| | - Martin Hovland
- Department of Biology, University of Bergen, PO Box 7803, 5020 Bergen, Norway.,Centre for Geobiology, University of Bergen, PO Box 7803, 5020 Bergen, Norway
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22
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Functional compartmentalization and metabolic separation in a prokaryotic cell. Proc Natl Acad Sci U S A 2021; 118:2022114118. [PMID: 34161262 DOI: 10.1073/pnas.2022114118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The prokaryotic cell is traditionally seen as a "bag of enzymes," yet its organization is much more complex than in this simplified view. By now, various microcompartments encapsulating metabolic enzymes or pathways are known for Bacteria These microcompartments are usually small, encapsulating and concentrating only a few enzymes, thus protecting the cell from toxic intermediates or preventing unwanted side reactions. The hyperthermophilic, strictly anaerobic Crenarchaeon Ignicoccus hospitalis is an extraordinary organism possessing two membranes, an inner and an energized outer membrane. The outer membrane (termed here outer cytoplasmic membrane) harbors enzymes involved in proton gradient generation and ATP synthesis. These two membranes are separated by an intermembrane compartment, whose function is unknown. Major information processes like DNA replication, RNA synthesis, and protein biosynthesis are located inside the "cytoplasm" or central cytoplasmic compartment. Here, we show by immunogold labeling of ultrathin sections that enzymes involved in autotrophic CO2 assimilation are located in the intermembrane compartment that we name (now) a peripheric cytoplasmic compartment. This separation may protect DNA and RNA from reactive aldehydes arising in the I. hospitalis carbon metabolism. This compartmentalization of metabolic pathways and information processes is unprecedented in the prokaryotic world, representing a unique example of spatiofunctional compartmentalization in the second domain of life.
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23
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Bhattacharya S, Roche R, Shuvo MH, Bhattacharya D. Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading. Front Mol Biosci 2021; 8:643752. [PMID: 34046429 PMCID: PMC8148041 DOI: 10.3389/fmolb.2021.643752] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
Sequence-based protein homology detection has emerged as one of the most sensitive and accurate approaches to protein structure prediction. Despite the success, homology detection remains very challenging for weakly homologous proteins with divergent evolutionary profile. Very recently, deep neural network architectures have shown promising progress in mining the coevolutionary signal encoded in multiple sequence alignments, leading to reasonably accurate estimation of inter-residue interaction maps, which serve as a rich source of additional information for improved homology detection. Here, we summarize the latest developments in protein homology detection driven by inter-residue interaction map threading. We highlight the emerging trends in distant-homology protein threading through the alignment of predicted interaction maps at various granularities ranging from binary contact maps to finer-grained distance and orientation maps as well as their combination. We also discuss some of the current limitations and possible future avenues to further enhance the sensitivity of protein homology detection.
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Affiliation(s)
- Sutanu Bhattacharya
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, United States
| | - Rahmatullah Roche
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, United States
| | - Md Hossain Shuvo
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, United States
| | - Debswapna Bhattacharya
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, United States
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
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Mahnert A, Verseux C, Schwendner P, Koskinen K, Kumpitsch C, Blohs M, Wink L, Brunner D, Goessler T, Billi D, Moissl-Eichinger C. Microbiome dynamics during the HI-SEAS IV mission, and implications for future crewed missions beyond Earth. MICROBIOME 2021; 9:27. [PMID: 33487169 PMCID: PMC7831191 DOI: 10.1186/s40168-020-00959-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/06/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Human health is closely interconnected with its microbiome. Resilient microbiomes in, on, and around the human body will be key for safe and successful long-term space travel. However, longitudinal dynamics of microbiomes inside confined built environments are still poorly understood. Herein, we used the Hawaii Space Exploration Analog and Simulation IV (HI-SEAS IV) mission, a 1 year-long isolation study, to investigate microbial transfer between crew and habitat, in order to understand adverse developments which may occur in a future outpost on the Moon or Mars. RESULTS Longitudinal 16S rRNA gene profiles, as well as quantitative observations, revealed significant differences in microbial diversity, abundance, and composition between samples of the built environment and its crew. The microbiome composition and diversity associated with abiotic surfaces was found to be rather stable, whereas the microbial skin profiles of individual crew members were highly dynamic, resulting in an increased microbiome diversity at the end of the isolation period. The skin microbiome dynamics were especially pronounced by a regular transfer of the indicator species Methanobrevibacter between crew members within the first 200 days. Quantitative information was used to track the propagation of antimicrobial resistance in the habitat. Together with functional and phenotypic predictions, quantitative and qualitative data supported the observation of a delayed longitudinal microbial homogenization between crew and habitat surfaces which was mainly caused by a malfunctioning sanitary facility. CONCLUSIONS This study highlights main routes of microbial transfer, interaction of the crew, and origins of microbial dynamics in an isolated environment. We identify key targets of microbial monitoring, and emphasize the need for defined baselines of microbiome diversity and abundance on surfaces and crew skin. Targeted manipulation to counteract adverse developments of the microbiome could be a highly important strategy to ensure safety during future space endeavors. Video abstract.
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Affiliation(s)
- Alexander Mahnert
- Interactive Microbiome Research, Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Cyprien Verseux
- Laboratory of Applied Space Microbiology, Center of Applied Space Technology and Microgravity (ZARM), University of Bremen, Am Fallturm 2, 28359 Bremen, Germany
| | - Petra Schwendner
- University of Florida, Space Life Sciences Lab, 505 Odyssey Way, Exploration Park, N. Merritt Island, FL 32953 USA
| | - Kaisa Koskinen
- Interactive Microbiome Research, Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Christina Kumpitsch
- Interactive Microbiome Research, Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Marcus Blohs
- Interactive Microbiome Research, Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Lisa Wink
- Interactive Microbiome Research, Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Daniela Brunner
- Interactive Microbiome Research, Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Theodora Goessler
- Interactive Microbiome Research, Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Daniela Billi
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica s.n.c, 00133 Rome, Italy
| | - Christine Moissl-Eichinger
- Interactive Microbiome Research, Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
- BioTechMed-Graz, Graz, Austria
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25
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Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep 2021; 38:130-239. [PMID: 32935693 PMCID: PMC7864896 DOI: 10.1039/d0np00027b] [Citation(s) in RCA: 362] [Impact Index Per Article: 120.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
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Metagenomes from Experimental Hydrologic Manipulation of Restored Coastal Plain Wetland Soils (Tyrell County, North Carolina). Microbiol Resour Announc 2020; 9:9/41/e00882-20. [PMID: 33033130 PMCID: PMC7545284 DOI: 10.1128/mra.00882-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hydrologic changes modify microbial community structure and ecosystem functions, especially in wetland systems. Here, we present 24 metagenomes from a coastal freshwater wetland experiment in which we manipulated hydrologic conditions and plant presence. These wetland soil metagenomes will deepen our understanding of how hydrology and vegetation influence microbial functional diversity. Hydrologic changes modify microbial community structure and ecosystem functions, especially in wetland systems. Here, we present 24 metagenomes from a coastal freshwater wetland experiment in which we manipulated hydrologic conditions and plant presence. These wetland soil metagenomes will deepen our understanding of how hydrology and vegetation influence microbial functional diversity.
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27
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Watanabe M, Higashioka Y, Kojima H, Fukui M. Proposal of Desulfosarcina ovata subsp. sediminis subsp. nov., a novel toluene-degrading sulfate-reducing bacterium isolated from tidal flat sediment of Tokyo Bay. Syst Appl Microbiol 2020; 43:126109. [PMID: 32847784 DOI: 10.1016/j.syapm.2020.126109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 11/30/2022]
Abstract
Strain 28bB2TT is a sulfate-reducing bacterium isolated in a previous study, obtained from a p-xylene-degrading enrichment culture. Physiological, phylogenetic and genomic characterizations of strain 28bB2TT were performed to establish the taxonomic status of the strain. Cells of strain 28bB2TT were short oval-shaped (0.8-1.2×1.2-2.7μm), motile, and Gram-negative. For growth, the optimum pH was pH 6.5-7.0 and the optimum temperature was 28-32°C. Strain 28bB2TT oxidized toluene but could not utilize p-xylene. Sulfate and thiosulfate were used as electron acceptors. The G+C content of the genomic DNA was 53.8mol%. The genome consisted of an approximately 8.3 Mb of chromosome and two extrachromosomal elements. On the basis of 16S rRNA gene analysis, strain 28bB2TT was revealed to belong to the genus Desulfosarcina, with high sequence identities to Desulfosarcina ovata oXyS1T (99.5%) and Desulfosarcina cetonica DSM 7267T (98.7%). Results of Average Nucleotide Identity (ANI) calculation and digital DNA-DNA hybridization (dDDH) analysis showed that the strain 28bB2TT should be classified as a subspecies under D. ovata. Based on physiological and phylogenetic data, strain 28bB2TT (=NBRC 106234 =DSM 23484) is proposed as the type strain of a novel species in genus Desulfosarcina, Desulfosarcina ovata subsp. sediminis subsp. nov.
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Affiliation(s)
- Miho Watanabe
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido, Japan; Postdoctoral Research Fellow of the Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-8471, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan; Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
| | - Yuriko Higashioka
- National Institute of Technology, Kochi College, 200-1 Otsu, Monobe, Nankoku-city, Kochi 783-8508, Japan
| | - Hisaya Kojima
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido, Japan
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28
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Kanger K, Guilford NGH, Lee H, Nesbø CL, Truu J, Edwards EA. Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard. FEMS Microbiol Ecol 2020; 96:5700280. [PMID: 31922542 DOI: 10.1093/femsec/fiaa006] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/09/2020] [Indexed: 11/13/2022] Open
Abstract
Solid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here, we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-state anaerobic digester treating a mixture of food waste, paper and cardboard. A total of 10 samples from digester feed and digestion products were collected for microbial community analysis including small subunit rRNA gene sequencing, total community metagenome sequencing and high-throughput quantitative PCR. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. ARGs were identified in all samples with multidrug resistance being the most abundant ARG type. Thirty-two per cent of ARGs detected in digester feed were located on plasmids indicating potential for horizontal gene transfer. Using metagenomic assembly and binning, we detected potential bacterial hosts of ARGs in digester feed, which included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.
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Affiliation(s)
- Kärt Kanger
- Faculty of Science and Technology, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Nigel G H Guilford
- BioZone Centre for Applied Biosciences and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - HyunWoo Lee
- BioZone Centre for Applied Biosciences and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - Camilla L Nesbø
- BioZone Centre for Applied Biosciences and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada.,Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
| | - Jaak Truu
- Faculty of Science and Technology, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Elizabeth A Edwards
- BioZone Centre for Applied Biosciences and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
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29
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Fungus-growing insects host a distinctive microbiota apparently adapted to the fungiculture environment. Sci Rep 2020; 10:12384. [PMID: 32709946 PMCID: PMC7381635 DOI: 10.1038/s41598-020-68448-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 06/24/2020] [Indexed: 01/09/2023] Open
Abstract
Some lineages of ants, termites, and beetles independently evolved a symbiotic association with lignocellulolytic fungi cultivated for food, in a lifestyle known as fungiculture. Fungus-growing insects' symbiosis also hosts a bacterial community thought to integrate their physiology. Similarities in taxonomic composition support the microbiota of fungus-growing insects as convergent, despite differences in fungus-rearing by these insects. Here, by comparing fungus-growing insects to several hosts ranging diverse dietary patterns, we investigate whether the microbiota taxonomic and functional profiles are characteristic of the fungiculture environment. Compared to other hosts, the microbiota associated with fungus-growing insects presents a distinctive taxonomic profile, dominated by Gammaproteobacteria at class level and by Pseudomonas at genera level. Even with a functional profile presenting similarities with the gut microbiota of herbivorous and omnivorous hosts, some differentially abundant features codified by the microbiota of fungus-growing insects suggest these communities occupying microhabitats that are characteristic of fungiculture. These features include metabolic pathways involved in lignocellulose breakdown, detoxification of plant secondary metabolites, metabolism of simple sugars, fungal cell wall deconstruction, biofilm formation, antimicrobials biosynthesis, and metabolism of diverse nutrients. Our results suggest that the microbiota could be functionally adapted to the fungiculture environment, codifying metabolic pathways potentially relevant to the fungus-growing insects' ecosystems functioning.
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30
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Cullings K, Stott MB, Marinkovich N, DeSimone J, Bhardwaj S. Phylum-level diversity of the microbiome of the extremophilic basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert: An island of biodiversity in a thermal soil desert. Microbiologyopen 2020; 9:e1062. [PMID: 32478485 PMCID: PMC7424252 DOI: 10.1002/mbo3.1062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 11/16/2022] Open
Abstract
We used high‐throughput DNA sequencing methods combined with bio‐geochemical profiles to characterize the internal environment and community structure of the microbiome of the basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert from soils within a geothermal feature of Yellowstone National Park. Pisolithus arhizus is unique in that it forms closed fruiting bodies that sequester visible sulfur within. Fourier transform infrared spectroscopy (FTIR) analysis demonstrates that the P. arhizus fruiting body also concentrates copper, manganese, nickel, and zinc and contains pure granular silica. Gas chromatography‐mass spectrometry (GC‐MS) analysis indicates an environment rich in hydrocarbons. Oxygen probe analysis reveals that zones of up to 4× atmospheric oxygen exist within nanometers of zones of near anoxia. Analysis of microbial community structure using high‐throughput DNA sequencing methods shows that the fruiting body supports a microbiome that reflects the physiochemical environment of the fruiting body. Diversity and richness measures indicate a microbiome that is significantly richer and more diverse than that of the soils in which P. arhizus grows. Further, P. arhizus sporocarps are enriched significantly in Proteobacteria (primarily Burkholderia) Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Nitrospirae, Elusimicrobia, and Latescibacteria (WS3) while soils are enriched in Actinobacteria (primarily Mycobacterium), Dormibacteraeota (AD3), and Eremiobacteraeota (WPS‐2). Finally, pairwise % similarity comparisons indicate that P. arhizus harbors two lineages that may represent new groups in the candidate phylum radiation (CPR). Together, these results demonstrate that P. arhizus provides a novel environment for microbiome studies and provides for interesting hypotheses regarding the evolution, origins, and functions of symbioses and novel microbes.
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Affiliation(s)
- Ken Cullings
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Julia DeSimone
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
| | - Shilpa Bhardwaj
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
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31
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Garcia MO, Templer PH, Sorensen PO, Sanders-DeMott R, Groffman PM, Bhatnagar JM. Soil Microbes Trade-Off Biogeochemical Cycling for Stress Tolerance Traits in Response to Year-Round Climate Change. Front Microbiol 2020; 11:616. [PMID: 32477275 PMCID: PMC7238748 DOI: 10.3389/fmicb.2020.00616] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/19/2020] [Indexed: 01/16/2023] Open
Abstract
Winter air temperatures are rising faster than summer air temperatures in high-latitude forests, increasing the frequency of soil freeze/thaw events in winter. To determine how climate warming and soil freeze/thaw cycles affect soil microbial communities and the ecosystem processes they drive, we leveraged the Climate Change across Seasons Experiment (CCASE) at the Hubbard Brook Experimental Forest in the northeastern United States, where replicate field plots receive one of three climate treatments: warming (+5°C above ambient in the growing season), warming in the growing season + winter freeze/thaw cycles (+5°C above ambient +4 freeze/thaw cycles during winter), and no treatment. Soil samples were taken from plots at six time points throughout the growing season and subjected to amplicon (rDNA) and metagenome sequencing. We found that soil fungal and bacterial community composition were affected by changes in soil temperature, where the taxonomic composition of microbial communities shifted more with the combination of growing-season warming and increased frequency of soil freeze/thaw cycles in winter than with warming alone. Warming increased the relative abundance of brown rot fungi and plant pathogens but decreased that of arbuscular mycorrhizal fungi, all of which recovered under combined growing-season warming and soil freeze/thaw cycles in winter. The abundance of animal parasites increased significantly under combined warming and freeze/thaw cycles. We also found that warming and soil freeze/thaw cycles suppressed bacterial taxa with the genetic potential for carbon (i.e., cellulose) decomposition and soil nitrogen cycling, such as N fixation and the final steps of denitrification. These new soil communities had higher genetic capacity for stress tolerance and lower genetic capacity to grow or reproduce, relative to the communities exposed to warming in the growing season alone. Our observations suggest that initial suppression of biogeochemical cycling with year-round climate change may be linked to the emergence of taxa that trade-off growth for stress tolerance traits.
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Affiliation(s)
- Maria O. Garcia
- Department of Biology, Boston University, Boston, MA, United States
| | | | - Patrick O. Sorensen
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Rebecca Sanders-DeMott
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Peter M. Groffman
- Advanced Science Research Center at the Graduate Center, City University of New York, New York, NY, United States
- Cary Institute of Ecosystem Studies, Millbrook, NY, United States
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Kamalanathan M, Doyle SM, Xu C, Achberger AM, Wade TL, Schwehr K, Santschi PH, Sylvan JB, Quigg A. Exoenzymes as a Signature of Microbial Response to Marine Environmental Conditions. mSystems 2020; 5:e00290-20. [PMID: 32291350 PMCID: PMC7159900 DOI: 10.1128/msystems.00290-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/01/2020] [Indexed: 01/14/2023] Open
Abstract
Microbial heterotopic metabolism in the ocean is fueled by a supply of essential nutrients acquired via exoenzymes catalyzing depolymerization of high-molecular-weight compounds. Although the rates of activity for a variety of exoenzymes across various marine environments are well established, the factors regulating the production of these exoenzymes, and to some extent their correlation with microbial community composition, are less known. This study focuses on addressing these challenges using a mesocosm experiment that compared a natural seawater microbial community (control) and exposed (to oil) treatment. Exoenzyme activities for β-glucosidase, leucine aminopeptidase (LAP), and lipase were significantly correlated with dissolved nutrient concentrations. We measured correlations between carbon- and nitrogen-acquiring enzymes (β-glucosidase/lipase versus LAP) and found that the correlation of carbon-acquiring enzymes varies with the chemical nature of the available primary carbon source. Notably, a strong correlation between particulate organic carbon and β-glucosidase activity demonstrates their polysaccharide depolymerization in providing the carbon for microbial growth. Last, we show that exoenzyme activity patterns are not necessarily correlated with prokaryotic community composition, suggesting a redundancy of exoenzyme functions among the marine microbial community and substrate availability. This study provides foundational work for linking exoenzyme function with dissolved organic substrate and downstream processes in marine systems.IMPORTANCE Microbes release exoenzymes into the environment to break down complex organic matter and nutrients into simpler forms that can be assimilated and utilized, thereby addressing their cellular carbon, nitrogen, and phosphorus requirements. Despite its importance, the factors associated with the synthesis of exoenzymes are not clearly defined, especially for the marine environment. Here, we found that exoenzymes associated with nitrogen and phosphorus acquisition were strongly correlated with inorganic nutrient levels, while those associated with carbon acquisition depended on the type of organic carbon available. We also show a linear relationship between carbon- and nitrogen-acquiring exoenzymes and a strong correlation between microbial biomass and exoenzymes, highlighting their significance to microbial productivity. Last, we show that changes in microbial community composition are not strongly associated with changes in exoenzyme activity profiles, a finding which reveals a redundancy of exoenzyme activity functions among microbial community. These findings advance our understanding of previously unknown factors associated with exoenzyme production in the marine environment.
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Affiliation(s)
- Manoj Kamalanathan
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, Texas, USA
| | - Shawn M Doyle
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
| | - Chen Xu
- Department of Marine Science, Texas A&M University at Galveston, Galveston, Texas, USA
| | - Amanda M Achberger
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
| | - Terry L Wade
- Geochemical and Environmental Research Group, Texas A&M University, College Station, Texas, USA
| | - Kathy Schwehr
- Department of Marine Science, Texas A&M University at Galveston, Galveston, Texas, USA
| | - Peter H Santschi
- Department of Marine Science, Texas A&M University at Galveston, Galveston, Texas, USA
| | - Jason B Sylvan
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
| | - Antonietta Quigg
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, Texas, USA
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
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33
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Metagenomes in the Borderline Ecosystems of the Antarctic Cryptoendolithic Communities. Microbiol Resour Announc 2020; 9:9/10/e01599-19. [PMID: 32139564 PMCID: PMC7171226 DOI: 10.1128/mra.01599-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Antarctic cryptoendolithic communities are microbial ecosystems dwelling inside rocks of the Antarctic desert. We present the first 18 shotgun metagenomes from these communities to further characterize their composition, biodiversity, functionality, and adaptation. Future studies will integrate taxonomic and functional annotations to examine the pathways necessary for life to evolve in the extremes. Antarctic cryptoendolithic communities are microbial ecosystems dwelling inside rocks of the Antarctic desert. We present the first 18 shotgun metagenomes from these communities to further characterize their composition, biodiversity, functionality, and adaptation. Future studies will integrate taxonomic and functional annotations to examine the pathways necessary for life to evolve in the extremes.
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34
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Sousa STPD, Cabral L, Lacerda-Júnior GV, Noronha MF, Ottoni JR, Sartoratto A, Oliveira VMD. Exploring the genetic potential of a fosmid metagenomic library from an oil-impacted mangrove sediment for metabolism of aromatic compounds. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 189:109974. [PMID: 31761556 DOI: 10.1016/j.ecoenv.2019.109974] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/10/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
Aromatic hydrocarbons (AH) are widely distributed in nature, and many of them have been reported as relevant environmental pollutants and valuable carbon sources for different microorganisms. In this work, high-throughput sequencing of a metagenomic fosmid library was carried out to evaluate the functional and taxonomic diversity of genes involved in aromatic compounds degradation in oil-impacted mangrove sediments. In addition, activity-based approach and gas chromatography were used to assess the degradation potential of fosmid clones. Results indicated that AH degradation genes, such as monooxygenases and dioxygenases, were grouped into the following categories: anaerobic degradation of aromatic compounds (20.34%), metabolism of central aromatic intermediates (35.40%) and peripheral pathways for catabolism of aromatic compounds (22.56%). Taxonomic affiliation of genes related to aromatic compounds metabolism revealed the prevalence of the classes Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria. Aromatic hydrocarbons (phenol, naphthalene, phenanthrene, pyrene and benzopyrene) were used as the only carbon source to screen clones with degradation potential. Of the 2500 clones tested, 48 showed some respiratory activity in at least one of the five carbon sources used. The hydrocarbon degradation ability of the top ten fosmid clones was confirmed by GC-MS. Further, annotation of assembled metagenomic fragments revealed ORFs corresponding to proteins and functional domains directly or indirectly involved in the aromatic compound metabolism, such as catechol 2,3-dioxygenase and ferredoxin oxidoreductase. Finally, these data suggest that the indigenous mangrove sediment microbiota developed essential mechanisms towards ecosystem remediation of petroleum hydrocarbon impact.
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Affiliation(s)
- Sanderson Tarciso Pereira de Sousa
- Research Center for Chemistry, Biology and Agriculture (CPQBA), Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Lucélia Cabral
- Research Center for Chemistry, Biology and Agriculture (CPQBA), Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Gileno Vieira Lacerda-Júnior
- Research Center for Chemistry, Biology and Agriculture (CPQBA), Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Melline Fontes Noronha
- Research Center for Chemistry, Biology and Agriculture (CPQBA), Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Júlia Ronzella Ottoni
- Research Center for Chemistry, Biology and Agriculture (CPQBA), Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Adilson Sartoratto
- Research Center for Chemistry, Biology and Agriculture (CPQBA), Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Valéria Maia de Oliveira
- Research Center for Chemistry, Biology and Agriculture (CPQBA), Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
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Posttranslational Methylation of Arginine in Methyl Coenzyme M Reductase Has a Profound Impact on both Methanogenesis and Growth of Methanococcus maripaludis. J Bacteriol 2020; 202:JB.00654-19. [PMID: 31740491 DOI: 10.1128/jb.00654-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/09/2019] [Indexed: 02/05/2023] Open
Abstract
Catalyzing the key step for anaerobic production and/or oxidation of methane and likely other short-chain alkanes, methyl coenzyme M reductase (Mcr) and its homologs play a key role in the global carbon cycle. The McrA subunit possesses up to five conserved posttranslational modifications (PTMs) at its active site. It was previously suggested that methanogenesis marker protein 10 (Mmp10) could play an important role in methanogenesis. To systematically examine its physiological role, mmpX (locus tag MMP1554), the gene encoding Mmp10 in Methanococcus maripaludis, was deleted with a new genetic tool, resulting in the complete loss of the 5-C-(S)-methylarginine PTM of residue 275 in the McrA subunit. When the ΔmmpX mutant was complemented with the wild-type gene expressed by either a strong or a weak promoter, methylation was fully restored. Compared to the parental strain, maximal rates of methane formation by whole cells were reduced by 40 to 60% in the ΔmmpX mutant. The reduction in activity was fully reversed by the complement with the strong promoter. Site-directed mutagenesis of mmpX resulted in a differential loss of arginine methylation among the mutants in vivo, suggesting that activities of Mmp10 directly modulated methylation. R275 was present in a highly conserved PXRR275(A/S)R(G/A) signature sequence in McrAs. The only other protein in M. maripaludis containing a similar sequence was not methylated, suggesting that Mmp10 is specific for McrA. In conclusion, Mmp10 modulates the methyl-Arg PTM on McrA in a highly specific manner, which has a profound impact on Mcr activity.IMPORTANCE Mcr is the key enzyme in methanogenesis and a promising candidate for bioengineering the conversion of methane to liquid fuel. Our knowledge of Mcr is still limited. In terms of complexity, uniqueness, and environmental importance, Mcr is more comparable to photosynthetic reaction centers than conventional enzymes. PTMs have long been hypothesized to play key roles in modulating Mcr activity. Here, we directly link the mmpX gene to the arginine PTM of Mcr, demonstrate its association with methanogenesis activity, and offer insights into its substrate specificity and putative cofactor binding sites. This is also the first time that a PTM of McrA has been shown to have a substantial impact on both methanogenesis and growth in the absence of additional stressors.
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Lucaciu R, Pelikan C, Gerner SM, Zioutis C, Köstlbacher S, Marx H, Herbold CW, Schmidt H, Rattei T. A Bioinformatics Guide to Plant Microbiome Analysis. FRONTIERS IN PLANT SCIENCE 2019; 10:1313. [PMID: 31708944 PMCID: PMC6819368 DOI: 10.3389/fpls.2019.01313] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/20/2019] [Indexed: 05/18/2023]
Abstract
Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant-microbiome studies. We discuss sequencing and "omics" techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant-bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.
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Affiliation(s)
| | | | | | | | | | | | | | - Hannes Schmidt
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
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Davenport EJ, Neudeck MJ, Matson PG, Bullerjahn GS, Davis TW, Wilhelm SW, Denney MK, Krausfeldt LE, Stough JMA, Meyer KA, Dick GJ, Johengen TH, Lindquist E, Tringe SG, McKay RML. Metatranscriptomic Analyses of Diel Metabolic Functions During a Microcystis Bloom in Western Lake Erie (United States). Front Microbiol 2019; 10:2081. [PMID: 31551998 PMCID: PMC6746948 DOI: 10.3389/fmicb.2019.02081] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/23/2019] [Indexed: 12/02/2022] Open
Abstract
This study examined diel shifts in metabolic functions of Microcystis spp. during a 48-h Lagrangian survey of a toxin-producing cyanobacterial bloom in western Lake Erie in the aftermath of the 2014 Toledo Water Crisis. Transcripts mapped to the genomes of recently sequenced lower Great Lakes Microcystis isolates showed distinct patterns of gene expression between samples collected across day (10:00 h, 16:00 h) and night (22:00 h, 04:00 h). Daytime transcripts were enriched in functions related to Photosystem II (e.g., psbA), nitrogen and phosphate acquisition, cell division (ftsHZ), heat shock response (dnaK, groEL), and uptake of inorganic carbon (rbc, bicA). Genes transcribed during nighttime included those involved in phycobilisome protein synthesis and Photosystem I core subunits. Hierarchical clustering and principal component analysis (PCA) showed a tightly clustered group of nighttime expressed genes, whereas daytime transcripts were separated from each other over the 48-h duration. Lack of uniform clustering within the daytime transcripts suggested that the partitioning of gene expression in Microcystis is dependent on both circadian regulation and physicochemical changes within the environment.
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Affiliation(s)
- Emily J. Davenport
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States,Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, MI, United States
| | - Michelle J. Neudeck
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States
| | - Paul G. Matson
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States
| | - George S. Bullerjahn
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States,*Correspondence: George S. Bullerjahn,
| | - Timothy W. Davis
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States
| | - Steven W. Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Maddie K. Denney
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Lauren E. Krausfeldt
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Joshua M. A. Stough
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Kevin A. Meyer
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, MI, United States,Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Thomas H. Johengen
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, MI, United States
| | - Erika Lindquist
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Susannah G. Tringe
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Robert Michael L. McKay
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States,Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
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Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the pmoCAB Operon of Type Ia Methanotrophs. mSystems 2019; 4:4/4/e00342-19. [PMID: 31337658 PMCID: PMC6650546 DOI: 10.1128/msystems.00342-19] [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: 11/26/2022] Open
Abstract
Microbial methane oxidation plays a fundamental role in the biogeochemical cycle of Earth’s system. Recent reports have provided evidence for the acquisition of methane monooxygenases by horizontal gene transfer in methane-oxidizing bacteria from different environments, but how evolution has shaped the coding sequences to execute methanotrophy efficiently remains unexplored. In this work, we provide genomic evidence that among the different types of methanotrophs, type Ia methanotrophs possess a unique coding sequence of the pmoCAB operon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence. Understanding the interplay between genotype and phenotype is a fundamental goal of functional genomics. Methane oxidation is a microbial phenotype with global-scale significance as part of the carbon biogeochemical cycle and a sink for greenhouse gas. Microorganisms that oxidize methane (methanotrophs) are taxonomically diverse and widespread around the globe. In methanotrophic bacteria, enzymes in the methane oxidation metabolic module (KEGG module M00174, conversion of methane to formaldehyde) are encoded in four operons (pmoCAB, mmoXYZBCD, mxaFI, and xoxF). Recent reports have suggested that methanotrophs in Proteobacteria acquired methane monooxygenases through horizontal gene transfer. Here, we used a genomic meta-analysis to infer the transcriptional and translational advantages of coding sequences from the methane oxidation metabolic modules of different types of methanotrophs. By analyzing isolate and metagenome-assembled genomes from phylogenetically and geographically diverse sources, we detected an anomalous nucleotide composition bias in the coding sequences of particulate methane monooxygenase genes (pmoCAB) from type Ia methanotrophs. We found that this nucleotide bias increases the level of codon bias by decreasing the GC content in the third base of codons, a strategy that contrasts with that of other coding sequences in the module. Further codon usage analyses uncovered that codon variants of the type Ia pmoCAB coding sequences deviate from the genomic signature to match ribosomal protein-coding sequences. Subsequently, computation of transcription and translation metrics revealed that the pmoCAB coding sequences of type Ia methanotrophs optimize the usage of codon variants to maximize translation efficiency and accuracy, while minimizing the synthesis cost of transcripts and proteins. IMPORTANCE Microbial methane oxidation plays a fundamental role in the biogeochemical cycle of Earth’s system. Recent reports have provided evidence for the acquisition of methane monooxygenases by horizontal gene transfer in methane-oxidizing bacteria from different environments, but how evolution has shaped the coding sequences to execute methanotrophy efficiently remains unexplored. In this work, we provide genomic evidence that among the different types of methanotrophs, type Ia methanotrophs possess a unique coding sequence of the pmoCAB operon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence.
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Klasek SA, Torres ME, Loher M, Bohrmann G, Pape T, Colwell FS. Deep-Sourced Fluids From a Convergent Margin Host Distinct Subseafloor Microbial Communities That Change Upon Mud Flow Expulsion. Front Microbiol 2019; 10:1436. [PMID: 31281306 PMCID: PMC6596357 DOI: 10.3389/fmicb.2019.01436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/07/2019] [Indexed: 11/13/2022] Open
Abstract
Submarine mud volcanoes (MVs) along continental margins emit mud breccia and globally significant amounts of hydrocarbon-rich fluids from the subsurface, and host distinct chemosynthetic communities of microbes and macrofauna. Venere MV lies at 1,600 m water depth in the Ionian Sea offshore Italy and is located in a forearc basin of the Calabrian accretionary prism. Porewaters of recently extruded mud breccia flowing from its west summit are considerably fresher than seawater (10 PSU), high in Li+ and B (up to 300 and 8,000 μM, respectively), and strongly depleted in K+ (<1 mM) at depths as shallow as 20 cm below seafloor. These properties document upward transport of fluids sourced from >3 km below seafloor. 16S rRNA gene and metagenomic sequencing were used to characterize microbial community composition and gene content within deep-sourced mud breccia flow deposits as they become exposed to seawater along a downslope transect of Venere MV. Summit samples showed consistency in microbial community composition. However, beta-diversity increased markedly in communities from downslope cores, which were dominated by methyl- and methanotrophic genera of Gammaproteobacteria. Methane, sulfate, and chloride concentrations were minor but significant contributors to variation in community composition. Metagenomic analyses revealed differences in relative abundances of predicted protein categories between Venere MV and other subsurface microbial communities, characterizing MVs as windows into distinct deep biosphere habitats.
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Affiliation(s)
- Scott A Klasek
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States
| | - Marta E Torres
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| | - Markus Loher
- MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Gerhard Bohrmann
- MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Thomas Pape
- MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Frederick S Colwell
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States.,College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
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40
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Seah BKB, Antony CP, Huettel B, Zarzycki J, Schada von Borzyskowski L, Erb TJ, Kouris A, Kleiner M, Liebeke M, Dubilier N, Gruber-Vodicka HR. Sulfur-Oxidizing Symbionts without Canonical Genes for Autotrophic CO 2 Fixation. mBio 2019; 10:e01112-19. [PMID: 31239380 PMCID: PMC6593406 DOI: 10.1128/mbio.01112-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/23/2019] [Indexed: 01/25/2023] Open
Abstract
Since the discovery of symbioses between sulfur-oxidizing (thiotrophic) bacteria and invertebrates at hydrothermal vents over 40 years ago, it has been assumed that autotrophic fixation of CO2 by the symbionts drives these nutritional associations. In this study, we investigated "Candidatus Kentron," the clade of symbionts hosted by Kentrophoros, a diverse genus of ciliates which are found in marine coastal sediments around the world. Despite being the main food source for their hosts, Kentron bacteria lack the key canonical genes for any of the known pathways for autotrophic carbon fixation and have a carbon stable isotope fingerprint that is unlike other thiotrophic symbionts from similar habitats. Our genomic and transcriptomic analyses instead found metabolic features consistent with growth on organic carbon, especially organic and amino acids, for which they have abundant uptake transporters. All known thiotrophic symbionts have converged on using reduced sulfur to gain energy lithotrophically, but they are diverse in their carbon sources. Some clades are obligate autotrophs, while many are mixotrophs that can supplement autotrophic carbon fixation with heterotrophic capabilities similar to those in Kentron. Here we show that Kentron bacteria are the only thiotrophic symbionts that appear to be entirely heterotrophic, unlike all other thiotrophic symbionts studied to date, which possess either the Calvin-Benson-Bassham or the reverse tricarboxylic acid cycle for autotrophy.IMPORTANCE Many animals and protists depend on symbiotic sulfur-oxidizing bacteria as their main food source. These bacteria use energy from oxidizing inorganic sulfur compounds to make biomass autotrophically from CO2, serving as primary producers for their hosts. Here we describe a clade of nonautotrophic sulfur-oxidizing symbionts, "Candidatus Kentron," associated with marine ciliates. They lack genes for known autotrophic pathways and have a carbon stable isotope fingerprint heavier than other symbionts from similar habitats. Instead, they have the potential to oxidize sulfur to fuel the uptake of organic compounds for heterotrophic growth, a metabolic mode called chemolithoheterotrophy that is not found in other symbioses. Although several symbionts have heterotrophic features to supplement primary production, in Kentron they appear to supplant it entirely.
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Affiliation(s)
| | | | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jan Zarzycki
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Angela Kouris
- Energy Bioengineering and Geomicrobiology Group, University of Calgary, Calgary, Alberta, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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Ellegaard KM, Brochet S, Bonilla‐Rosso G, Emery O, Glover N, Hadadi N, Jaron KS, Meer JR, Robinson‐Rechavi M, Sentchilo V, Tagini F, Engel P. Genomic changes underlying host specialization in the bee gut symbiont
Lactobacillus
Firm5. Mol Ecol 2019; 28:2224-2237. [DOI: 10.1111/mec.15075] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/21/2019] [Accepted: 03/04/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Kirsten M. Ellegaard
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Silvia Brochet
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - German Bonilla‐Rosso
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Olivier Emery
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Natasha Glover
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | - Noushin Hadadi
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Kamil S. Jaron
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Jan R. Meer
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Marc Robinson‐Rechavi
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Florian Tagini
- Institute of Microbiology, Department of Laboratory Medicine University of Lausanne & Lausanne University Hospital Lausanne Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
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42
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Rossmassler K, Snow CD, Taggart D, Brown C, De Long SK. Advancing biomarkers for anaerobic o-xylene biodegradation via metagenomic analysis of a methanogenic consortium. Appl Microbiol Biotechnol 2019; 103:4177-4192. [PMID: 30968165 DOI: 10.1007/s00253-019-09762-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/07/2019] [Accepted: 03/10/2019] [Indexed: 10/27/2022]
Abstract
Quantifying functional biomarker genes and their transcripts provides critical lines of evidence for contaminant biodegradation; however, accurate quantification depends on qPCR primers that contain no, or minimal, mismatches with the target gene. Developing accurate assays has been particularly challenging for genes encoding fumarate-adding enzymes (FAE) due to the high level of genetic diversity in this gene family. In this study, metagenomics applied to a field-derived, o-xylene-degrading methanogenic consortium revealed genes encoding FAE that would not be accurately quantifiable by any previously available PCR assays. Sequencing indicated that a gene similar to the napthylmethylsuccinate synthase gene (nmsA) was most abundant, although benzylsuccinate synthase genes (bssA) also were present along with genes encoding alkylsuccinate synthase (assA). Upregulation of the nmsA-like gene was observed during o-xylene degradation. Protein homology modeling indicated that mutations in the active site, relative to a BssA that acts on toluene, increase binding site volume and accessibility, potentially to accommodate the relatively larger o-xylene. The new nmsA-like gene was also detected at substantial concentrations at field sites with a history of xylene contamination.
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Affiliation(s)
- Karen Rossmassler
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, USA.,Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Christopher D Snow
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
| | | | - Casey Brown
- Microbial Insights, Inc., Knoxville, TN, USA
| | - Susan K De Long
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, USA.
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Yin L, Harwood CS. Functional divergence of annotated l-isoaspartate O-methyltransferases in an α-proteobacterium. J Biol Chem 2019; 294:2854-2861. [PMID: 30578298 DOI: 10.1074/jbc.ra118.006546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/14/2018] [Indexed: 12/28/2022] Open
Abstract
Spontaneous formation of isoaspartates (isoDs) often causes protein damage. l-Isoaspartate O-methyltransferase (PIMT) repairs isoD residues by catalyzing the formation of an unstable l-isoaspartyl methyl ester that spontaneously converts to an l-aspartyl residue. PIMTs are widely distributed in all three domains of life and have been studied most intensively in connection with their role in protein repair and aging in plants and animals. Studies of bacterial PIMTs have been limited to Escherichia coli, which has one PIMT. The α-proteobacterium Rhodopseudomonas palustris has three annotated PIMT genes, one of which (rpa2580) has been found to be important for cellular longevity in a growth-arrested state. However, the biochemical activities of these three R. palustris PIMTs are unknown. Here, we expressed and characterized all three annotated PIMT proteins, finding that two of them, RPA0376 and RPA2838, had PIMT activity, whereas RPA2580 did not. RPA0376 and RPA2838 single- and double-deletion mutants did not differ in longevity from WT R. palustris and did not exhibit elevated levels of isoD residues in aged cells. Comparative sequence analyses revealed that RPA2580 belongs to a separate phylogenetic group of annotated PIMT proteins present in the α-proteobacteria. Our results suggest that this group of proteins is not involved in repair of protein isoD residues. In addition, the bona fide bacterial PIMT enzymes may play a different or subtler role in bacterial physiology than previously suggested.
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Affiliation(s)
- Liang Yin
- From the Department of Microbiology, University of Washington, Seattle, Washington 98195
| | - Caroline S Harwood
- From the Department of Microbiology, University of Washington, Seattle, Washington 98195
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Narihiro T, Kamagata Y. Genomics and Metagenomics in Microbial Ecology: Recent Advances and Challenges. Microbes Environ 2019; 32:1-4. [PMID: 28367917 PMCID: PMC5371069 DOI: 10.1264/jsme2.me3201rh] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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Watanabe M, Kojima H, Umezawa K, Fukui M. Genomic Characteristics of Desulfonema ishimotonii Tokyo 01 T Implying Horizontal Gene Transfer Among Phylogenetically Dispersed Filamentous Gliding Bacteria. Front Microbiol 2019; 10:227. [PMID: 30837965 PMCID: PMC6390638 DOI: 10.3389/fmicb.2019.00227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/28/2019] [Indexed: 11/13/2022] Open
Abstract
Desulfonema ishimotonii strain Tokyo 01T is a filamentous sulfate-reducing bacterium isolated from a marine sediment. In this study, the genome of this strain was sequenced and analyzed with a focus on gene transfer from phylogenetically distant organisms. While the strain belongs to the class Deltaproteobacteria, hundreds of proteins encoded in the genome showed the highest sequence similarities to those of organisms outside of the class Deltaproteobacteria, suggesting that more than 20% of the genome is putatively of foreign origins. Many of these proteins had the highest sequence identities with proteins encoded in the genomes of filamentous bacteria, including giant sulfur oxidizers of the orders Thiotrichales, cyanobacteria of various genera, and uncultured bacteria of the candidate phylum KSB3. As mobile genetic elements transferred from phylogenetically distant organisms, putative inteins were identified in the GyrB and DnaE proteins encoded in the genome of strain Tokyo 01T. Genes involved in DNA recombination and repair were enriched in comparison to the closest relatives in the same family. Some of these genes were also related to those of organisms outside of the class Deltaproteobacteria, suggesting that they were acquired by horizontal gene transfer from diverse bacteria. The genomic data suggested significant genetic transfer among filamentous gliding bacteria in phylogenetically dispersed lineages including filamentous sulfate reducers. This study provides insights into the genomic evolution of filamentous bacteria belonging to diverse lineages, characterized by various physiological functions and different ecological roles.
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Affiliation(s)
- Miho Watanabe
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.,Japan Society for the Promotion of Science, Tokyo, Japan
| | - Hisaya Kojima
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Kazuhiro Umezawa
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
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46
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Lambrechts S, Willems A, Tahon G. Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach. Front Microbiol 2019; 10:242. [PMID: 30828325 PMCID: PMC6385771 DOI: 10.3389/fmicb.2019.00242] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/29/2019] [Indexed: 01/22/2023] Open
Abstract
Although Antarctica was once believed to be a sterile environment, it is now clear that the microbial communities inhabiting the Antarctic continent are surprisingly diverse. Until the beginning of the new millennium, little was known about the most abundant inhabitants of the continent: prokaryotes. From then on, however, the rising use of deep sequencing techniques has led to a better understanding of the Antarctic prokaryote diversity and provided insights in the composition of prokaryotic communities in different Antarctic environments. Although these cultivation-independent approaches can produce millions of sequences, linking these data to organisms is hindered by several problems. The largest difficulty is the lack of biological information on large parts of the microbial tree of life, arising from the fact that most microbial diversity on Earth has never been characterized in laboratory cultures. These unknown prokaryotes, also known as microbial dark matter, have been dominantly detected in all major environments on our planet. Laboratory cultures provide access to the complete genome and the means to experimentally verify genomic predictions and metabolic functions and to provide evidence of horizontal gene transfer. Without such well-documented reference data, microbial dark matter will remain a major blind spot in deep sequencing studies. Here, we review our current understanding of prokaryotic communities in Antarctic ice-free soils based on cultivation-dependent and cultivation-independent approaches. We discuss advantages and disadvantages of both approaches and how these strategies may be combined synergistically to strengthen each other and allow a more profound understanding of prokaryotic life on the frozen continent.
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Affiliation(s)
- Sam Lambrechts
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | | | - Guillaume Tahon
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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Thiel V, Garcia Costas AM, Fortney NW, Martinez JN, Tank M, Roden EE, Boyd ES, Ward DM, Hanada S, Bryant DA. " Candidatus Thermonerobacter thiotrophicus," A Non-phototrophic Member of the Bacteroidetes/Chlorobi With Dissimilatory Sulfur Metabolism in Hot Spring Mat Communities. Front Microbiol 2019; 9:3159. [PMID: 30687241 PMCID: PMC6338057 DOI: 10.3389/fmicb.2018.03159] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/05/2018] [Indexed: 12/31/2022] Open
Abstract
In this study we present evidence for a novel, thermophilic bacterium with dissimilatory sulfur metabolism, tentatively named “Candidatus Thermonerobacter thiotrophicus,” which is affiliated with the Bacteroides/Ignavibacteria/Chlorobi and which we predict to be a sulfate reducer. Dissimilatory sulfate reduction (DSR) is an important and ancient metabolic process for energy conservation with global importance for geochemical sulfur and carbon cycling. Characterized sulfate-reducing microorganisms (SRM) are found in a limited number of bacterial and archaeal phyla. However, based on highly diverse environmental dsrAB sequences, a variety of uncultivated and unidentified SRM must exist. The recent development of high-throughput sequencing methods allows the phylogenetic identification of some of these uncultured SRM. In this study, we identified a novel putative SRM inhabiting hot spring microbial mats that is a member of the OPB56 clade (“Ca. Kapabacteria”) within the Bacteroidetes/Chlorobi superphylum. Partial genomes for this new organism were retrieved from metagenomes from three different hot springs in Yellowstone National Park, United States, and Japan. Supporting the prediction of a sulfate-reducing metabolism for this organism during period of anoxia, diel metatranscriptomic analyses indicate highest relative transcript levels in situ for all DSR-related genes at night. The presence of terminal oxidases, which are transcribed during the day, further suggests that these organisms might also perform aerobic respiration. The relative phylogenetic proximity to the sulfur-oxidizing, chlorophototrophic Chlorobi further raises new questions about the evolution of dissimilatory sulfur metabolism.
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Affiliation(s)
- Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Amaya M Garcia Costas
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States.,Department of Biology, Colorado State University-Pueblo, Pueblo, CO, United States
| | - Nathaniel W Fortney
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, United States
| | - Joval N Martinez
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Natural Sciences, University of St. La Salle, Bacolod, Philippines
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, United States
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States.,Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
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48
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Calderoli PA, Espínola FJ, Dionisi HM, Gil MN, Jansson JK, Lozada M. Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution. PLoS One 2018; 13:e0207606. [PMID: 30496195 PMCID: PMC6264515 DOI: 10.1371/journal.pone.0207606] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 11/02/2018] [Indexed: 11/20/2022] Open
Abstract
The aim of this work was to characterize the microbial nitrogen cycling potential in sediments from Ushuaia Bay, a subantarctic environment that has suffered a recent explosive demographic growth. Subtidal sediment samples were retrieved in triplicate from two urban points in the Bay, and analyzed through metagenomic shotgun sequencing. Sequences assigned to genes related to nitrification, nitrate reduction and denitrification were predominant in this environment with respect to metagenomes from other environments, including other marine sediments. The nosZ gene, responsible for nitrous oxide transformation into di-nitrogen, presented a high diversity. The majority of NosZ sequences were classified as Clade II (atypical) variants affiliated to different bacterial lineages such as Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, Verrucomicrobia, as well as to Archaea. The analysis of a fosmid metagenomic library from the same site showed that the genomic context of atypical variants was variable, and was accompanied by distinct regulatory elements, suggesting the evolution of differential ecophysiological roles. This work increases our understanding of the microbial ecology of nitrogen transformations in cold coastal environments and provides evidence of an enhanced denitrification potential in impacted sediment microbial communities. In addition, it highlights the role of yet overlooked populations in the mitigation of environmentally harmful forms of nitrogen.
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Affiliation(s)
- Priscila A Calderoli
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Fernando J Espínola
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Mónica N Gil
- Laboratorio de Oceanografía Química y Contaminación de Aguas, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina.,Laboratorio de Química General y Análisis de Elementos, CCT CONICET CENPAT, Puerto Madryn, Chubut Province, Argentina
| | - Janet K Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
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Mejia J, He S, Yang Y, Ginder-Vogel M, Roden EE. Stability of Ferrihydrite-Humic Acid Coprecipitates under Iron-Reducing Conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:13174-13183. [PMID: 30354092 PMCID: PMC8381759 DOI: 10.1021/acs.est.8b03615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Recent studies have suggested the potential for release of iron (hydr)oxide-bound organic carbon (OC) during dissimilatory iron oxide reduction (DIR). However, the stability of iron (hydr)oxide-bound OC in the presence of a natural microbial consortium capable of driving both OC metabolism and DIR has not been resolved. Pure ferrihydrite (Fhy) and Fhy-humic acid coprecipitates (Fhy-HA) were inoculated with a small quantity of freshwater sediment and incubated under anoxic conditions in the presence and absence of H2 or glucose as electron donors for DIR. H2 promoted DIR led to release of ca. 1 mM dissolved organic carbon (DOC). However, comparable amounts of DOC were released from both pure Fhy and Fhy-HA, similar to DOC levels in mineral-free, inoculum-only controls. These results suggest that the observed DOC release during H2-promoted DIR originated from OC contained in the inoculum as opposed to the much larger pool (ca. 38 mM) of OC in the Fhy-HA. Thus, DIR preferentially released sorbed OC with low aromaticity (inoculum OC) versus highly aromatic OC (HA) coprecipitated with iron oxide. Our findings provide new insight into the extent and mechanisms by which DIR is likely to influence aqueous/solid-phase OC partitioning in anoxic soils and sediments.
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Affiliation(s)
- Jacqueline Mejia
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Shaomei He
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yu Yang
- Department of Civil and Environmental Engineering, University of Nevada-Reno, Reno, NV, 89557, USA
| | - Matthew Ginder-Vogel
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI 53706, USA
- Corresponding Author: Eric E. Roden. , Phone: 608-890-7024. Fax: 608-262-0693
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50
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Harrington LB, Burstein D, Chen JS, Paez-Espino D, Ma E, Witte IP, Cofsky JC, Kyrpides NC, Banfield JF, Doudna JA. Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science 2018; 362:839-842. [PMID: 30337455 PMCID: PMC6659742 DOI: 10.1126/science.aav4294] [Citation(s) in RCA: 583] [Impact Index Per Article: 97.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 10/06/2018] [Indexed: 12/18/2022]
Abstract
CRISPR-Cas systems provide microbes with adaptive immunity to infectious nucleic acids and are widely employed as genome editing tools. These tools use RNA-guided Cas proteins whose large size (950 to 1400 amino acids) has been considered essential to their specific DNA- or RNA-targeting activities. Here we present a set of CRISPR-Cas systems from uncultivated archaea that contain Cas14, a family of exceptionally compact RNA-guided nucleases (400 to 700 amino acids). Despite their small size, Cas14 proteins are capable of targeted single-stranded DNA (ssDNA) cleavage without restrictive sequence requirements. Moreover, target recognition by Cas14 triggers nonspecific cutting of ssDNA molecules, an activity that enables high-fidelity single-nucleotide polymorphism genotyping (Cas14-DETECTR). Metagenomic data show that multiple CRISPR-Cas14 systems evolved independently and suggest a potential evolutionary origin of single-effector CRISPR-based adaptive immunity.
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Affiliation(s)
- Lucas B Harrington
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - David Burstein
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
| | - Janice S Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - David Paez-Espino
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Enbo Ma
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Isaac P Witte
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Joshua C Cofsky
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jillian F Banfield
- 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
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
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