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Tan S, Liu J, Fang Y, Hedlund BP, Lian ZH, Huang LY, Li JT, Huang LN, Li WJ, Jiang HC, Dong HL, Shu WS. Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics. THE ISME JOURNAL 2019; 13:2044-2057. [PMID: 30962514 PMCID: PMC6776010 DOI: 10.1038/s41396-019-0415-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/15/2019] [Accepted: 03/24/2019] [Indexed: 12/21/2022]
Abstract
Several abundant but yet uncultivated bacterial groups exist in extreme iron- and sulfur-rich environments, and the physiology, biodiversity, and ecological roles of these bacteria remain a mystery. Here we retrieved four metagenome-assembled genomes (MAGs) from an artificial acid mine drainage (AMD) system, and propose they belong to a new deltaproteobacterial order, Candidatus Acidulodesulfobacterales. The distribution pattern of Ca. Acidulodesulfobacterales in AMDs across Southeast China correlated strongly with ferrous iron. Reconstructed metabolic pathways and gene expression profiles showed that they were likely facultatively anaerobic autotrophs capable of nitrogen fixation. In addition to dissimilatory sulfate reduction, encoded by dsrAB, dsrD, dsrL, and dsrEFH genes, these microorganisms might also oxidize sulfide, depending on oxygen concentration and/or oxidation reduction potential. Several genes with homology to those involved in iron metabolism were also identified, suggesting their potential role in iron cycling. In addition, the expression of abundant resistance genes revealed the mechanisms of adaptation and response to the extreme environmental stresses endured by these organisms in the AMD environment. These findings shed light on the distribution, diversity, and potential ecological role of the new order Ca. Acidulodesulfobacterales in nature.
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Affiliation(s)
- Sha Tan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jun Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, 45056, USA
| | - Yun Fang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Zheng-Han Lian
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
- Guangdong Magigene Biotechnology Co. Ltd., 510000, Guangzhou, China
| | - Li-Ying Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jin-Tian Li
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Hai-Liang Dong
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, 45056, USA.
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 100083, Beijing, China.
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China.
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Gagliano AL, Tagliavia M, D'Alessandro W, Franzetti A, Parello F, Quatrini P. So close, so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites. GEOBIOLOGY 2016; 14:150-162. [PMID: 26560641 DOI: 10.1111/gbi.12167] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 10/01/2015] [Indexed: 06/05/2023]
Abstract
This study is focused on the (micro)biogeochemical features of two close geothermal sites (FAV1 and FAV2), both selected at the main exhalative area of Pantelleria Island, Italy. A previous biogeochemical survey revealed high CH4 consumption and the presence of a diverse community of methanotrophs at FAV2 site, whereas the close site FAV1 was apparently devoid of methanotrophs and recorded no CH4 consumption. Next-Generation Sequencing (NGS) techniques were applied to describe the bacterial and archaeal communities which have been linked to the physicochemical conditions and the geothermal sources of energy available at the two sites. Both sites are dominated by Bacteria and host a negligible component of ammonia-oxidizing Archaea (phylum Thaumarchaeota). The FAV2 bacterial community is characterized by an extraordinary diversity of methanotrophs, with 40% of the sequences assigned to Methylocaldum, Methylobacter (Gammaproteobacteria) and Bejerickia (Alphaproteobacteria); conversely, a community of thermo-acidophilic chemolithotrophs (Acidithiobacillus, Nitrosococcus) or putative chemolithotrophs (Ktedonobacter) dominates the FAV1 community, in the absence of methanotrophs. Since physical andchemical factors of FAV1, such as temperature and pH, cannot be considered limiting for methanotrophy, it is hypothesized that the main limiting factor for methanotrophs could be high NH4(+) concentration. At the same time, abundant availability of NH4(+) and other high energy electron donors and acceptors determined by the hydrothermal flux in this site create more energetically favourable conditions for chemolithotrophs that outcompete methanotrophs in non-nitrogen-limited soils.
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Affiliation(s)
- A L Gagliano
- Istituto Nazionale di Geofisica e Vulcanologia (INGV) - Sezione di Palermo, Palermo, Italy
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, Palermo, Italy
| | - M Tagliavia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
- Institute for Coastal Marine Environment (CNR-IAMC) U.O.S. of Capo Granitola, Campobello di Mazara, Italy
| | - W D'Alessandro
- Istituto Nazionale di Geofisica e Vulcanologia (INGV) - Sezione di Palermo, Palermo, Italy
| | - A Franzetti
- Department of Earth and Environmental Sciences, University of Milano- Bicocca, Milano, Italy
| | - F Parello
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, Palermo, Italy
| | - P Quatrini
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
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Pukall R, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Mavromatis K, Ivanova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Meincke L, Sims D, Brettin T, Detter JC, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Kyrpides NC, Klenk HP, Hugenholtz P. Complete genome sequence of Conexibacter woesei type strain (ID131577). Stand Genomic Sci 2010; 2:212-9. [PMID: 21304704 PMCID: PMC3035278 DOI: 10.4056/sigs.751339] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The genus Conexibacter (Monciardini et al. 2003) represents the type genus of the family Conexibacteraceae (Stackebrandt 2005, emend. Zhi et al. 2009) with Conexibacter woesei as the type species of the genus. C. woesei is a representative of a deep evolutionary line of descent within the class Actinobacteria. Strain ID131577T was originally isolated from temperate forest soil in Gerenzano (Italy). Cells are small, short rods that are motile by peritrichous flagella. They may form aggregates after a longer period of growth and, then as a typical characteristic, an undulate structure is formed by self-aggregation of flagella with entangled bacterial cells. Here we describe the features of the organism, together with the complete sequence and annotation. The 6,359,369 bp long genome of C. woesei contains 5,950 protein-coding and 48 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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