1
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Chen X, Liu S, Song H, Yuan C, Li J. Evaluation of biological activity and prebiotic properties of proanthocyanidins with different degrees of polymerization through simulated digestion and in vitro fermentation by human fecal microbiota. Food Chem 2024; 447:139015. [PMID: 38513492 DOI: 10.1016/j.foodchem.2024.139015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/27/2024] [Accepted: 03/10/2024] [Indexed: 03/23/2024]
Abstract
The bioactive activity of proanthocyanidins (PAs) is closely associated with their degree of polymerization (DP), however, the effects of PAs with different DP on digestion and gut microbiota have remained unclear. To investigate this, we conducted in vitro simulated digestion and colonic fermentation studies on samples of PAs with different DP. The results showed that PAs was influenced by both protein precipitation and enzymolysis, resulting in a decrease in functional activity. PAs with a high DP were more sensitive to the gastrointestinal environment. The significant clustering trend in colonic fermentation verified the reliability of multivariate statistical techniques for screening samples with distinct functional differences. The gut microbiota analysis showed that oligomeric PAs had a stronger promoting effect on beneficial bacteria, while high polymeric PAs had a greater inhibitory effect on harmful bacteria. This study offers new insights into the biological activity and microbiological mechanisms of PAs with different DP.
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Affiliation(s)
- Xiaoyi Chen
- College of Enology, Northwest A&F University, Shaanxi 712100, China
| | - Shuai Liu
- College of Enology, Northwest A&F University, Shaanxi 712100, China
| | - Hong Song
- College of Enology, Northwest A&F University, Shaanxi 712100, China
| | - Chunlong Yuan
- College of Enology, Northwest A&F University, Shaanxi 712100, China; Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station of Northwest A&F University, Yongning, Ningxia 750104, China.
| | - Junjun Li
- College of Enology, Northwest A&F University, Shaanxi 712100, China.
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2
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Liu YH, Gao L, Jiang HC, Fang BZ, Huang Y, Li L, Li S, Abdugheni R, Lian WH, Zhang JY, Yang ZD, Mohamad OAA, Li WJ. Response of microbial diversity and function to the degradation of Barkol Saline Lake. Front Microbiol 2024; 15:1358222. [PMID: 38784797 PMCID: PMC11111964 DOI: 10.3389/fmicb.2024.1358222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Barkol Lake, a shrinking hypersaline lake situated in the northeast of Xinjiang, China, has experienced the exposure of its riverbed and the gradual drying up of its original sediment due to climate change and human activities, resulting in the formation of alkaline soils. These changes have correspondingly altered the physicochemical characteristics of the surrounding environment. Microorganisms play a crucial role, with special functioning involved in various nutrient cycling and energy transfer in saline lake environments. However, little is known about how the microbial community dynamics and metabolic functions in this shrinking saline lake relate to the degradation process. To address this knowledge gap, a cultivation-independent method of amplicon sequencing was used to identify and analyze the microbial community and its potential ecological functions in the sediment and degraded area. The microbial community diversity was found to be significantly lower in the degraded areas than in the sediment samples. The Pseudomonadota was dominant in Barkol Saline Lake. The abundance of Desulfobacterota and Bacillota in the degraded areas was lower than in the lake sediment, while Pseudomonadota, Acidobacteriota, and Actinobacteriota showed an opposite trend. The βNTI showed that microbial community assembly was primarily associated with deterministic processes in Barkol Saline Lake ecosystems and stochastic processes at the boundary between sediment and degraded areas. Functional predictions showed that sulfur metabolism, particularly sulfate respiration, was much higher in sediment samples than in the degraded areas. Overall, these findings provided a possible perspective for us to understand how microorganisms adapt to extreme environments and their role in saline lakes under environmental change.
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Affiliation(s)
- Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Lei Gao
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Hong-Chen Jiang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Yin Huang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Shuai Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jing-Yi Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhen-Dong Yang
- School of Architecture and Civil Engineering, Chengdu University, Chengdu, China
| | - Osama Abdalla Abdelshafy Mohamad
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Department of Biological, Marine Sciences and Environmental Agriculture, Institute for Post Graduate Environmental Studies, Arish University, Arish, Egypt
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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3
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Üstüntürk-Onan M, Tüccar T, Ilhan-Sungur E. Occurrence of sulfate-reducing bacteria in well water: identification of anaerobic sulfidogenic bacterial enrichment cultures. JOURNAL OF WATER AND HEALTH 2024; 22:746-756. [PMID: 38678427 DOI: 10.2166/wh.2024.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/15/2024] [Indexed: 04/30/2024]
Abstract
Bacteriological studies of well water mainly focus on aerobic and facultative aerobic coliform bacteria. However, the presence of obligate anaerobic bacteria in well water, especially sulfate-reducing bacteria (SRB), possible causative agents of some diseases, is often ignored. In this study, the presence of SRB and coexisting anaerobic bacteria with SRB in sulfate-reducing enrichment cultures obtained from 10 well water samples in Istanbul was investigated. A nested polymerase chain reaction-denaturing gradient gel electrophoresis strategy was performed to characterize the bacterial community structure of the enrichments. The most probable number method was used to determine SRB number. Out of 10, SRB growth was observed in only one (10%) enrichment culture and the SRB number was low (<10 cells/mL). Community members were identified as Desulfolutivibrio sulfodismutans and Anaerosinus sp. The results show that SRB coexist with Anaerosinus sp., and this may indicate poor water quality, posing a risk to public health. Furthermore, Anaerosinus sp., found in the human intestinal tract, may be used as an alternative anaerobic fecal indicator. It is worth noting that the detection of bacteria using molecular analyzes following enrichment culture techniques can bring new perspectives to determine the possible origin and presence of alternative microbial indicators in aquatic environments.
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Affiliation(s)
- Miray Üstüntürk-Onan
- Department of Biology, Faculty of Science, Istanbul University, Vezneciler, Istanbul 34134, Türkiye
| | - Tuğçe Tüccar
- Medical Laboratory Techniques Program, Vocational School, Istanbul Arel University, Cevizlibağ, Istanbul 34010, Türkiye E-mail:
| | - Esra Ilhan-Sungur
- Department of Biology, Faculty of Science, Istanbul University, Vezneciler, Istanbul 34134, Türkiye
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4
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Clausen U, Vital ST, Lambertus P, Gehler M, Scheve S, Wöhlbrand L, Rabus R. Catabolic Network of the Fermentative Gut Bacterium Phocaeicola vulgatus (Phylum Bacteroidota) from a Physiologic-Proteomic Perspective. Microb Physiol 2024; 34:88-107. [PMID: 38262373 DOI: 10.1159/000536327] [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: 08/28/2023] [Accepted: 01/10/2024] [Indexed: 01/25/2024]
Abstract
INTRODUCTION Phocaeicola vulgatus (formerly Bacteroides vulgatus) is a prevalent member of human and animal guts, where it influences by its dietary-fiber-fueled, fermentative metabolism the microbial community as well as the host health. Moreover, the fermentative metabolism of P. vulgatus bears potential for a sustainable production of bulk chemicals. The aim of the present study was to refine the current understanding of the P. vulgatus physiology. METHODS P. vulgatus was adapted to anaerobic growth with 14 different carbohydrates, ranging from hexoses, pentoses, hemicellulose, via an uronic acid to deoxy sugars. These substrate-adapted cells formed the basis to define the growth stoichiometries by quantifying growth/fermentation parameters and to reconstruct the catabolic network by applying differential proteomics. RESULTS The determination of growth performance revealed, e.g., doubling times (h) from 1.39 (arabinose) to 14.26 (glucuronate), biomass yields (gCDW/mmolS) from 0.01 (fucose) to 0.27 (α-cyclodextrin), and ATP yields (mMATP/mMC) from 0.21 (rhamnose) to 0.60 (glucuronate/xylan). Furthermore, fermentation product spectra were determined, ranging from broad and balanced (with xylan: acetate, succinate, formate, and propanoate) to rather one sided (with rhamnose or fucose: mainly propane-1,2-diol). The fermentation network serving all tested compounds is composed of 56 proteins (all identified), with several peripheral reaction sequences formed with high substrate specificity (e.g., conversion of arabinose to d-xylulose-3-phosphate) implicating a fine-tuned regulation. By contrast, central modules (e.g., glycolysis or the reaction sequence from PEP to succinate) were constitutively formed. Extensive formation of propane-1,2-diol from rhamnose and fucose involves rhamnulokinase (RhaB), rhamnulose-1-phosphate kinase (RhaD), and lactaldehyde reductase (FucO). Furthermore, Sus-like systems are apparently the most relevant uptake systems and a complex array of transmembrane electron-transfer systems (e.g., Na+-pumping Rnf and Nqr complexes, fumarate reductase) as well as F- and V-type ATP-synthases were detected. CONCLUSIONS The present study provides insights into the potential contribution of P. vulgatus to the gut metabolome and into the strain's biotechnological potential for sustainable production of short-chain fatty acids and alcohols.
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Affiliation(s)
- Urte Clausen
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Sören-Tobias Vital
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Pia Lambertus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Martina Gehler
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Sabine Scheve
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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5
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Oliveira AR, Mota C, Vilela-Alves G, Manuel RR, Pedrosa N, Fourmond V, Klymanska K, Léger C, Guigliarelli B, Romão MJ, Cardoso Pereira IA. An allosteric redox switch involved in oxygen protection in a CO 2 reductase. Nat Chem Biol 2024; 20:111-119. [PMID: 37985883 DOI: 10.1038/s41589-023-01484-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/12/2023] [Indexed: 11/22/2023]
Abstract
Metal-dependent formate dehydrogenases reduce CO2 with high efficiency and selectivity, but are usually very oxygen sensitive. An exception is Desulfovibrio vulgaris W/Sec-FdhAB, which can be handled aerobically, but the basis for this oxygen tolerance was unknown. Here we show that FdhAB activity is controlled by a redox switch based on an allosteric disulfide bond. When this bond is closed, the enzyme is in an oxygen-tolerant resting state presenting almost no catalytic activity and very low formate affinity. Opening this bond triggers large conformational changes that propagate to the active site, resulting in high activity and high formate affinity, but also higher oxygen sensitivity. We present the structure of activated FdhAB and show that activity loss is associated with partial loss of the metal sulfido ligand. The redox switch mechanism is reversible in vivo and prevents enzyme reduction by physiological formate levels, conferring a fitness advantage during O2 exposure.
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Affiliation(s)
- Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cristiano Mota
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Guilherme Vilela-Alves
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Rita Rebelo Manuel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Neide Pedrosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Vincent Fourmond
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Kateryna Klymanska
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Christophe Léger
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Bruno Guigliarelli
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Maria João Romão
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal.
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal.
| | - Inês A Cardoso Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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Dyksma S, Pester M. Oxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium. Nat Commun 2023; 14:6337. [PMID: 37816749 PMCID: PMC10564751 DOI: 10.1038/s41467-023-42074-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Sulfate-reducing microorganisms represent a globally important link between the sulfur and carbon cycles. Recent metagenomic surveys expanded the diversity of microorganisms putatively involved in sulfate reduction underscoring our incomplete understanding of this functional guild. Here, we use genome-centric metatranscriptomics to study the energy metabolism of Acidobacteriota that carry genes for dissimilation of sulfur compounds in a long-term continuous culture running under alternating anoxic and oxic conditions. Differential gene expression analysis reveals the unique metabolic flexibility of a pectin-degrading acidobacterium to switch from sulfate to oxygen reduction when shifting from anoxic to oxic conditions. The combination of facultative anaerobiosis and polysaccharide degradation expands the metabolic versatility among sulfate-reducing microorganisms. Our results highlight that sulfate reduction and aerobic respiration are not mutually exclusive in the same organism, sulfate reducers can mineralize organic polymers, and anaerobic mineralization of complex organic matter is not necessarily a multi-step process involving different microbial guilds but can be bypassed by a single microbial species.
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Affiliation(s)
- Stefan Dyksma
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Microorganisms, Braunschweig, Germany.
| | - Michael Pester
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Microorganisms, Braunschweig, Germany.
- Technical University of Braunschweig, Institute of Microbiology, Braunschweig, Germany.
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7
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Diao M, Dyksma S, Koeksoy E, Ngugi DK, Anantharaman K, Loy A, Pester M. Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction. FEMS Microbiol Rev 2023; 47:fuad058. [PMID: 37796897 PMCID: PMC10591310 DOI: 10.1093/femsre/fuad058] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/07/2023] Open
Abstract
Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB. Based on analysis of 950 mainly metagenome-derived dsrAB-carrying genomes, we redefine the global diversity of microorganisms with the potential for dissimilatory sulfate/sulfite reduction and uncover genetic repertoires that challenge earlier generalizations regarding their mode of energy metabolism. We show: (i) 19 out of 23 bacterial and 2 out of 4 archaeal phyla harbor uncharacterized SRM, (ii) four phyla including the Desulfobacterota harbor microorganisms with the genetic potential to switch between sulfate/sulfite reduction and sulfur oxidation, and (iii) the combination as well as presence/absence of different dsrAB-types, dsrL-types and dsrD provides guidance on the inferred direction of dissimilatory sulfur metabolism. We further provide an updated dsrAB database including > 60% taxonomically resolved, uncultured family-level lineages and recommendations on existing dsrAB-targeted primers for environmental surveys. Our work summarizes insights into the inferred ecophysiology of newly discovered SRM, puts SRM diversity into context of the major recent changes in bacterial and archaeal taxonomy, and provides an up-to-date framework to study SRM in a global context.
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Affiliation(s)
- Muhe Diao
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - Stefan Dyksma
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - Elif Koeksoy
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - David Kamanda Ngugi
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna A-1030, Austria
| | - Michael Pester
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
- Technical University of Braunschweig, Institute of Microbiology, Braunschweig D-38106, Germany
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8
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Gao P, Zhang X, Huang X, Chen Z, Marietou A, Holmkvist L, Qu L, Finster K, Gong X. Genomic insight of sulfate reducing bacterial genus Desulfofaba reveals their metabolic versatility in biogeochemical cycling. BMC Genomics 2023; 24:209. [PMID: 37076818 PMCID: PMC10116758 DOI: 10.1186/s12864-023-09297-2] [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: 08/11/2022] [Accepted: 04/04/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND Sulfate-reducing bacteria (SRB) drive the ocean sulfur and carbon cycling. They constitute a diverse phylogenetic and physiological group and are widely distributed in anoxic marine environments. From a physiological viewpoint, SRB's can be categorized as complete or incomplete oxidizers, meaning that they either oxidize their carbon substrate completely to CO2 or to a stoichiometric mix of CO2 and acetate. Members of Desulfofabaceae family are incomplete oxidizers, and within that family, Desulfofaba is the only genus with three isolates that are classified into three species. Previous physiological experiments revealed their capability of respiring oxygen. RESULTS Here, we sequenced the genomes of three isolates in Desulfofaba genus and reported on a genomic comparison of the three species to reveal their metabolic potentials. Based on their genomic contents, they all could oxidize propionate to acetate and CO2. We confirmed their phylogenetic position as incomplete oxidizers based on dissimilatory sulfate reductase (DsrAB) phylogeny. We found the complete pathway for dissimilatory sulfate reduction, but also different key genes for nitrogen cycling, including nitrogen fixation, assimilatory nitrate/nitrite reduction, and hydroxylamine reduction to nitrous oxide. Their genomes also contain genes that allow them to cope with oxygen and oxidative stress. They have genes that encode for diverse central metabolisms for utilizing different substrates with the potential for more strains to be isolated in the future, yet their distribution is limited. CONCLUSIONS Results based on marker gene search and curated metagenome assembled genomes search suggest a limited environmental distribution of this genus. Our results reveal a large metabolic versatility within the Desulfofaba genus which establishes their importance in biogeochemical cycling of carbon in their respective habitats, as well as in the support of the entire microbial community through releasing easily degraded organic matters.
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Affiliation(s)
- Ping Gao
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), 266061, Qingdao, PR China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, 266237, Qingdao, PR China
| | - Xiaoting Zhang
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China
| | - Xiaomei Huang
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China
| | - Zhiyi Chen
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China
| | - Angeliki Marietou
- Section for Microbiology, Department of Biology, Aarhus University, 8000, Aarhus, Denmark
- Department of Biological and Chemical Engineering, Aarhus University, 8000, Aarhus, Denmark
| | - Lars Holmkvist
- Section for Microbiology, Department of Biology, Aarhus University, 8000, Aarhus, Denmark
| | - Lingyun Qu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), 266061, Qingdao, PR China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, 266237, Qingdao, PR China
| | - Kai Finster
- Section for Microbiology, Department of Biology, Aarhus University, 8000, Aarhus, Denmark
- Stellar Astrophysics Center, Department of Physics and Astronomy, Aarhus University, 8000, Aarhus, Denmark
| | - Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China.
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9
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Barton LL, Duarte AG, Staicu LC. Genomic insight into iron acquisition by sulfate-reducing bacteria in microaerophilic environments. Biometals 2023; 36:339-350. [PMID: 35767096 DOI: 10.1007/s10534-022-00410-8] [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: 10/29/2021] [Accepted: 06/08/2022] [Indexed: 11/30/2022]
Abstract
Historically, sulfate-reducing bacteria (SRB) have been considered to be strict anaerobes, but reports in the past couple of decades indicate that SRB tolerate exposure to O2 and can even grow in aerophilic environments. With the transition from anaerobic to microaerophilic conditions, the uptake of Fe(III) from the environment by SRB would become important. In evaluating the metabolic capability for the uptake of iron, the genomes of 26 SRB, representing eight families, were examined. All SRB reviewed carry genes (feoA and feoB) for the ferrous uptake system to transport Fe(II) across the plasma membrane into the cytoplasm. In addition, all of the SRB genomes examined have putative genes for a canonical ABC transporter that may transport ferric siderophore or ferric chelated species from the environment. Gram-negative SRB have additional machinery to import ferric siderophores and ferric chelated species since they have the TonB system that can work alongside any of the outer membrane porins annotated in the genome. Included in this review is the discussion that SRB may use the putative siderophore uptake system to import metals other than iron.
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Affiliation(s)
- Larry L Barton
- Department of Biology, University of New Mexico, MSCO3 2020, Albuquerque, NM, 87131, USA
| | - Americo G Duarte
- Instituto de Tecnologia Química E Biológica António Xavier/Universidade NOVA de Lisboa, Av. República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Lucian C Staicu
- Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.
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10
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Bryukhanov AL, Khijniak TV. The Application of Sulfate-Reducing Bacteria in the Bioremediation of Heavy Metals and Metalloids. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822100039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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11
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Enrichment of Anaerobic Microbial Communities from Midgut and Hindgut of Sun Beetle Larvae (Pachnoda marginata) on Wheat Straw: Effect of Inoculum Preparation. Microorganisms 2022; 10:microorganisms10040761. [PMID: 35456811 PMCID: PMC9024811 DOI: 10.3390/microorganisms10040761] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 12/05/2022] Open
Abstract
The Pachnoda marginata larva have complex gut microbiota capable of the effective conversion of lignocellulosic biomass. Biotechnological utilization of these microorganisms in an engineered system can be achieved by establishing enrichment cultures using a lignocellulosic substrate. We established enrichment cultures from contents of the midgut and hindgut of the beetle larva using wheat straw in an alkaline medium at mesophilic conditions. Two different inoculation preparations were used: procedure 1 (P1) was performed in a sterile bench under oxic conditions using 0.4% inoculum and small gauge needles. Procedure 2 (P2) was carried out under anoxic conditions using more inoculum (4%) and bigger gauge needles. Higher methane production was achieved with P2, while the highest acetic acid concentrations were observed with P1. In the enrichment cultures, the most abundant bacterial families were Dysgonomonadaceae, Heliobacteriaceae, Ruminococcaceae, and Marinilabiliaceae. Further, the most abundant methanogenic genera were Methanobrevibacter, Methanoculleus, and Methanosarcina. Our observations suggest that in samples processed with P1, the volatile fatty acids were not completely converted to methane. This is supported by the finding that enrichment cultures obtained with P2 included acetoclastic methanogens, which might have prevented the accumulation of acetic acid. We conclude that differences in the inoculum preparation may have a major influence on the outcome of enrichment cultures from the P. marginata larvae gut.
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12
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Banker RMW, Lipovac J, Stachowicz JJ, Gold DA. Sodium molybdate does not inhibit sulfate-reducing bacteria but increases shell growth in the Pacific oyster Magallana gigas. PLoS One 2022; 17:e0262939. [PMID: 35139090 PMCID: PMC8827440 DOI: 10.1371/journal.pone.0262939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/07/2022] [Indexed: 11/23/2022] Open
Abstract
Recent work on microbe-host interactions has revealed an important nexus between the environment, microbiome, and host fitness. Marine invertebrates that build carbonate skeletons are of particular interest in this regard because of predicted effects of ocean acidification on calcified organisms, and the potential of microbes to buffer these impacts. Here we investigate the role of sulfate-reducing bacteria, a group well known to affect carbonate chemistry, in Pacific oyster (Magallana gigas) shell formation. We reared oyster larvae to 51 days post fertilization and exposed organisms to control and sodium molybdate conditions, the latter of which is thought to inhibit bacterial sulfate reduction. Contrary to expectations, we found that sodium molybdate did not uniformly inhibit sulfate-reducing bacteria in oysters, and oysters exposed to molybdate grew larger shells over the experimental period. Additionally, we show that microbiome composition, host gene expression, and shell size were distinct between treatments earlier in ontogeny, but became more similar by the end of the experiment. Although additional testing is required to fully elucidate the mechanisms, our work provides preliminary evidence that M. gigas is capable of regulating microbiome dysbiosis caused by environmental perturbations, which is reflected in shell development.
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Affiliation(s)
- Roxanne M. W. Banker
- Department of Earth and Planetary Sciences, University of California, Davis, California, United States of America
| | - Jacob Lipovac
- Department of Earth and Planetary Sciences, University of California, Davis, California, United States of America
| | - John J. Stachowicz
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - David A. Gold
- Department of Earth and Planetary Sciences, University of California, Davis, California, United States of America
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13
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Berg JS, Ahmerkamp S, Pjevac P, Hausmann B, Milucka J, Kuypers MMM. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6517451. [PMID: 35094062 PMCID: PMC9075580 DOI: 10.1093/femsre/fuac006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 12/01/2022] Open
Abstract
Oxygen (O2) is the ultimate oxidant on Earth and its respiration confers such an energetic advantage that microorganisms have evolved the capacity to scavenge O2 down to nanomolar concentrations. The respiration of O2 at extremely low levels is proving to be common to diverse microbial taxa, including organisms formerly considered strict anaerobes. Motivated by recent advances in O2 sensing and DNA/RNA sequencing technologies, we performed a systematic review of environmental metatranscriptomes revealing that microbial respiration of O2 at nanomolar concentrations is ubiquitous and drives microbial activity in seemingly anoxic aquatic habitats. These habitats were key to the early evolution of life and are projected to become more prevalent in the near future due to anthropogenic-driven environmental change. Here, we summarize our current understanding of aerobic microbial respiration under apparent anoxia, including novel processes, their underlying biochemical pathways, the involved microorganisms, and their environmental importance and evolutionary origin.
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Affiliation(s)
- Jasmine S Berg
- Corrresponding author: Géopolis, Quartier Unil-Mouline, Université de Lausanne, 1015 Lausanne, Switzerland. E-mail:
| | - Soeren Ahmerkamp
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 2359, Germany
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna 1090, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1090, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna 1090, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna 1090, Austria
| | - Jana Milucka
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 2359, Germany
| | - Marcel M M Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 2359, Germany
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14
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Mori F, Umezawa Y, Kondo R, Nishihara GN, Wada M. Potential oxygen consumption and community composition of sediment bacteria in a seasonally hypoxic enclosed bay. PeerJ 2021; 9:e11836. [PMID: 34434647 PMCID: PMC8362671 DOI: 10.7717/peerj.11836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/01/2021] [Indexed: 01/04/2023] Open
Abstract
The dynamics of potential oxygen consumption at the sediment surface in a seasonally hypoxic bay were monitored monthly by applying a tetrazolium dye (2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl-2H-tetrazolium chloride [INT]) reduction assay to intact sediment core samples for two consecutive years (2012–2013). Based on the empirically determined correlation between INT reduction (INT-formazan formation) and actual oxygen consumption of sediment samples, we inferred the relative contribution of biological and non-biological (chemical) processes to the potential whole oxygen consumption in the collected sediment samples. It was demonstrated that both potentials consistently increased and reached a maximum during summer hypoxia in each year. For samples collected in 2012, amplicon sequence variants (ASVs) of the bacterial 16S rRNA genes derived from the sediment surface revealed a sharp increase in the relative abundance of sulfate reducing bacteria toward hypoxia. In addition, a notable shift in other bacterial compositions was observed before and after the INT assay incubation. It was Arcobacter (Arcobacteraceae, Campylobacteria), a putative sulfur-oxidizing bacterial genus, that increased markedly during the assay period in the summer samples. These findings have implications not only for members of Delta- and Gammaproteobacteria that are consistently responsible for the consumption of dissolved oxygen (DO) year-round in the sediment, but also for those that might grow rapidly in response to episodic DO supply on the sediment surface during midst of seasonal hypoxia.
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Affiliation(s)
- Fumiaki Mori
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan.,Institute for East China Sea Research, Organization for Marine Science and Technology, Nagasaki University, Nagasaki, Nagasaki, Japan.,Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kochi, Japan
| | - Yu Umezawa
- Department of Environmental Science on Biosphere, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Ryuji Kondo
- Department of Marine Science and Technology, Fukui Prefectural University, Fukui, Japan
| | - Gregory N Nishihara
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan.,Institute for East China Sea Research, Organization for Marine Science and Technology, Nagasaki University, Nagasaki, Nagasaki, Japan
| | - Minoru Wada
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan
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15
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Akinpelu EA, Ntwampe SKO, Fosso-Kankeu E, Nchu F, Angadam JO. Performance of microbial community dominated by Bacillus spp. in acid mine drainage remediation systems: A focus on the high removal efficiency of SO 4 2-, Al 3+, Cd 2+, Cu 2+, Mn 2+, Pb 2+, and Sr 2. Heliyon 2021; 7:e07241. [PMID: 34189300 PMCID: PMC8215182 DOI: 10.1016/j.heliyon.2021.e07241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/31/2021] [Accepted: 06/03/2021] [Indexed: 11/28/2022] Open
Abstract
A consortium of microbial community was used for the treatment of acid mine drainage wastewater laden with sulphate and heavy metals. The wastewater was treated in an anaerobic continuously stirred tank bioreactor. The microbial community activity increased the pH from 5.6 to 6.5, and improved sulphate removal up to 85% from an initial sulphate concentration of 8080 mg SO42−/L in a continuous mode, following enrichment for 21 d. The maximum heavy metal removal percentage was observed for Cd (98%), Al (97%), Mn (95%), Pb (94%), Sr (94%) and Cu (91%). The microbial community showed synergy between strictly anaerobic and facultative Firmicutes sp., which were responsible for the bioreactor performance. The biochemical reaction indicated the microbial community has a wider range of substrates dominated by metallo-aminopeptidases.
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Affiliation(s)
- Enoch A Akinpelu
- Bioresource Engineering Research Group (BioERG), Cape Peninsula University of Technology, Cape Town, 8000, South Africa.,Department of Horticultural Sciences, Cape Peninsula University of Technology, Bellville Campus, Symphony Way, PO Box 1906, Bellville 7535, South Africa
| | - Seteno K O Ntwampe
- Center of Excellence in Carbon-based Fuels, School of Chemical and Minerals Engineering, North-West University, P. Bag X60001 Potchefstroom 2520, South Africa
| | - Elvis Fosso-Kankeu
- Center of Excellence in Carbon-based Fuels, School of Chemical and Minerals Engineering, North-West University, P. Bag X60001 Potchefstroom 2520, South Africa
| | - Felix Nchu
- Department of Horticultural Sciences, Cape Peninsula University of Technology, Bellville Campus, Symphony Way, PO Box 1906, Bellville 7535, South Africa
| | - Justine O Angadam
- Bioresource Engineering Research Group (BioERG), Cape Peninsula University of Technology, Cape Town, 8000, South Africa
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16
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Sánchez-Soto MF, Cerqueda-García D, Alcántara-Hernández RJ, Falcón LI, Pech D, Árcega-Cabrera F, Aguirre-Macedo ML, García-Maldonado JQ. Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene. MICROBIAL ECOLOGY 2021; 81:908-921. [PMID: 33196853 DOI: 10.1007/s00248-020-01631-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (dsrB gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of Proteobacteria and Firmicutes across all the samples. However, Actinobacteria, Thermodesulfobacteria, and Chlorobi were also detected. Phylogenetic analysis indicated that unassigned dsrB sequences were related to Deltaproteobacteria and Nitrospirota superclusters, Euryarchaeota, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of dsrAB-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.
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Affiliation(s)
- Ma Fernanda Sánchez-Soto
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico
| | - Daniel Cerqueda-García
- Consorcio de Investigación del Golfo de México (CIGOM), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico
| | | | - Luisa I Falcón
- Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal, Mexico
| | - Daniel Pech
- Laboratorio de Biodiversidad Marina y Cambio Climático, El Colegio de la Frontera Sur, Campeche, Mexico
| | - Flor Árcega-Cabrera
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico
| | - Ma Leopoldina Aguirre-Macedo
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico.
| | - José Q García-Maldonado
- CONACYT-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México.
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17
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Li GX, Bao P. Transcriptomics analysis of the metabolic mechanisms of iron reduction induced by sulfate reduction mediated by sulfate-reducing bacteria. FEMS Microbiol Ecol 2021; 97:6095723. [PMID: 33439980 DOI: 10.1093/femsec/fiab005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 01/11/2021] [Indexed: 11/12/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) play an important role in sulfur, iron and carbon cycling. The majority of studies have illustrated the role of SRB in biogeochemical cycling in pure cultures. In this study, we established three SRB enrichment cultures (designated HL, NB and WC) from different paddy soils and conducted a transcriptomic analysis of their metabolic characteristics under sulfate and sulfate-free conditions. In the HL cultures, there was no sulfate consumption but ferrihydrite was reduced. This indicated that bacteria in the HL samples can reduce ferrihydrite and preferentially utilize ferrihydrite as the electron acceptor in the absence of both ferrihydrite and sulfate. Sulfate consumption was equal in the NB and the WC cultures, although more ferrihydrite was reduced in the NB cultures. Transcriptomics analysis showed that (i) upregulation of O-acetylserine sulfhydrylase gene expression indicating sulfate assimilation in the WC samples; (ii) the energy conservation trithionate pathway is commonly employed by SRB and (iii) sulfate not only enhanced iron reduction by its conversion to sulfide but also promoted enzymatic electron transfer via c-type cytochromes.
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Affiliation(s)
- Guo-Xiang Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Jimei Road 1799, Xiamen 361021, P. R. China.,Ningbo Urban Environment Observation and Station, Chinese Academy of Sciences, Zhongke Road 88, Ningbo 315800, P. R. China.,Center for Applied Geosciences (ZAG), Eberhard Karls University Tuebingen, Hölderlinstr. 12, Tuebingen 72076, Germany
| | - Peng Bao
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Jimei Road 1799, Xiamen 361021, P. R. China.,Ningbo Urban Environment Observation and Station, Chinese Academy of Sciences, Zhongke Road 88, Ningbo 315800, P. R. China
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18
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Kushkevych I, Hýžová B, Vítězová M, Rittmann SKMR. Microscopic Methods for Identification of Sulfate-Reducing Bacteria from Various Habitats. Int J Mol Sci 2021; 22:4007. [PMID: 33924516 PMCID: PMC8069399 DOI: 10.3390/ijms22084007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/31/2021] [Accepted: 04/03/2021] [Indexed: 12/01/2022] Open
Abstract
This paper is devoted to microscopic methods for the identification of sulfate-reducing bacteria (SRB). In this context, it describes various habitats, morphology and techniques used for the detection and identification of this very heterogeneous group of anaerobic microorganisms. SRB are present in almost every habitat on Earth, including freshwater and marine water, soils, sediments or animals. In the oil, water and gas industries, they can cause considerable economic losses due to their hydrogen sulfide production; in periodontal lesions and the colon of humans, they can cause health complications. Although the role of these bacteria in inflammatory bowel diseases is not entirely known yet, their presence is increased in patients and produced hydrogen sulfide has a cytotoxic effect. For these reasons, methods for the detection of these microorganisms were described. Apart from selected molecular techniques, including metagenomics, fluorescence microscopy was one of the applied methods. Especially fluorescence in situ hybridization (FISH) in various modifications was described. This method enables visual identification of SRB, determining their abundance and spatial distribution in environmental biofilms and gut samples.
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Affiliation(s)
- Ivan Kushkevych
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (B.H.); (M.V.)
| | - Blanka Hýžová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (B.H.); (M.V.)
| | - Monika Vítězová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (B.H.); (M.V.)
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, 1090 Wien, Austria
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19
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Qian Y, Xu M, Deng T, Hu W, He Z, Yang X, Wang B, Song D, Chen L, Huang Y, Sun G. Synergistic interactions of Desulfovibrio and Petrimonas for sulfate-reduction coupling polycyclic aromatic hydrocarbon degradation. JOURNAL OF HAZARDOUS MATERIALS 2021; 407:124385. [PMID: 33229269 DOI: 10.1016/j.jhazmat.2020.124385] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 10/15/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
Microbial sulfate-reduction coupling polycyclic aromatic hydrocarbon (PAH) degradation is an important process for the remediation of contaminated sediments. However, little is known about core players and their mechanisms in this process due to the complexity of PAH degradation and the large number of microorganisms involved. Here we analyzed potential core players in a black-odorous sediment using gradient-dilution culturing, isolation and genomic/metagenomic approaches. Along the dilution gradient, microbial PAH degradation and sulfate consumption were not decreased, and even a significant (p = 0.003) increase was observed in the degradation of phenanthrene although the microbial diversity declined. Two species, affiliated with Desulfovibrio and Petrimonas, were commonly present in all of the gradients as keystone taxa and showed as the dominant microorganisms in the single colony (SB8) isolated from the highest dilution culture with 93.49% and 4.73% of the microbial community, respectively. Desulfovibrio sp. SB8 and Petrimonas sp. SB8 could serve together as core players for sulfate-reduction coupling PAH degradation, in which Desulfovibrio sp. SB8 could degrade PAHs to hexahydro-2-naphthoyl through the carboxylation pathway while Petrimonas sp. SB8 might degrade intermediate metabolites of PAHs. This study provides new insights into the microbial sulfate-reduction coupling PAH degradation in black-odorous sediments.
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Affiliation(s)
- Youfen Qian
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Tongchu Deng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Wenzhe Hu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Zhili He
- Environmental Microbiomics Research Center and School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Xunan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Bin Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Da Song
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Letian Chen
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Youda Huang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Guoping Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
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Sulphate-Reducing Bacteria’s Response to Extreme pH Environments and the Effect of Their Activities on Microbial Corrosion. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11052201] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Sulphate-reducing bacteria (SRB) are dominant species causing corrosion of various types of materials. However, they also play a beneficial role in bioremediation due to their tolerance of extreme pH conditions. The application of sulphate-reducing bacteria (SRB) in bioremediation and control methods for microbiologically influenced corrosion (MIC) in extreme pH environments requires an understanding of the microbial activities in these conditions. Recent studies have found that in order to survive and grow in high alkaline/acidic condition, SRB have developed several strategies to combat the environmental challenges. The strategies mainly include maintaining pH homeostasis in the cytoplasm and adjusting metabolic activities leading to changes in environmental pH. The change in pH of the environment and microbial activities in such conditions can have a significant impact on the microbial corrosion of materials. These bacteria strategies to combat extreme pH environments and their effect on microbial corrosion are presented and discussed.
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21
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Schnaars V, Wöhlbrand L, Scheve S, Hinrichs C, Reinhardt R, Rabus R. Proteogenomic Insights into the Physiology of Marine, Sulfate-Reducing, Filamentous Desulfonema limicola and Desulfonema magnum. Microb Physiol 2021; 31:1-20. [PMID: 33611323 PMCID: PMC8315694 DOI: 10.1159/000513383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/19/2020] [Indexed: 11/19/2022]
Abstract
The genus Desulfonema belongs to the deltaproteobacterial family Desulfobacteraceae and comprises marine, sulfate-reducing bacteria that form filaments and move by gliding. This study reports on the complete, manually annotated genomes of Dn. limicola 5ac10T (6.91 Mbp; 6,207 CDS) and Dn. magnum 4be13T (8.03 Mbp; 9,970 CDS), integrated with substrate-specific proteome profiles (8 vs. 11). The richness in mobile genetic elements is shared with other Desulfobacteraceae members, corroborating horizontal gene transfer as major driver in shaping the genomes of this family. The catabolic networks of Dn. limicola and Dn. magnum have the following general characteristics: 98 versus 145 genes assigned (having genomic shares of 1.7 vs. 2.2%), 92.5 versus 89.7% proteomic coverage, and scattered gene clusters for substrate degradation and energy metabolism. The Dn. magnum typifying capacity for aromatic compound degradation (e.g., p-cresol, 3-phenylpropionate) requires 48 genes organized in operon-like structures (87.7% proteomic coverage; no homologs in Dn. limicola). The protein complements for aliphatic compound degradation, central pathways, and energy metabolism are highly similar between both genomes and were identified to a large extent (69-96%). The differential protein profiles revealed a high degree of substrate-specificity for peripheral reaction sequences (forming central intermediates), agreeing with the high number of sensory/regulatory proteins predicted for both strains. By contrast, central pathways and modules of the energy metabolism were constitutively formed under the tested substrate conditions. In accord with their natural habitats that are subject to fluctuating changes of physicochemical parameters, both Desulfonema strains are well equipped to cope with various stress conditions. Next to superoxide dismutase and catalase also desulfoferredoxin and rubredoxin oxidoreductase are formed to counter exposure to molecular oxygen. A variety of proteases and chaperones were detected that function in maintaining cellular homeostasis upon heat or cold shock. Furthermore, glycine betaine/proline betaine transport systems can respond to hyperosmotic stress. Gliding movement probably relies on twitching motility via type-IV pili or adventurous motility. Taken together, this proteogenomic study demonstrates the adaptability of Dn. limicola and Dn. magnum to its dynamic habitats by means of flexible catabolism and extensive stress response capacities.
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Affiliation(s)
- Vanessa Schnaars
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Sabine Scheve
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Christina Hinrichs
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Richard Reinhardt
- Max-Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany,
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22
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Microbial community compositions and sulfate-reducing bacterial profiles in malodorous urban canal sediments. Arch Microbiol 2021; 203:1981-1993. [PMID: 33528590 DOI: 10.1007/s00203-020-02157-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/16/2020] [Accepted: 12/03/2020] [Indexed: 01/04/2023]
Abstract
Anthropogenically impacted urban canals represent distinct freshwater ecosystems that could shape microbial communities in underlying sediments; however, knowledge of the relationships between environmental factors and microbial community compositions and their functions in such an environment is limited. This study characterized the microbial community compositions of malodorous canal sediments at six locations along the Saen Saep Canal in Thailand. 16S rRNA gene amplicon sequencing (MiSeq, Illumina) revealed dominant genera classified as fermentative bacteria, methanogens, and sulfate-reducing bacteria (SRB), all of which emphasized anaerobic environments. SRB, as the primary producers of malodorous hydrogen sulfide, accounted for 8.2-30.4% of the total sequences. dsrB gene clone libraries further identified the SRB species. A constrained correspondence analysis demonstrated a spatial pattern of SRB that correlated with physicochemical parameters in which nitrate and sulfate in sediments were the most influencing factors. Overall, a better understanding of the SRB and other related microorganisms in canal sediments can assist in the future implementation of appropriate olfactory abatement and management methodologies in urban canals.
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Scilipoti S, Koren K, Risgaard-Petersen N, Schramm A, Nielsen LP. Oxygen consumption of individual cable bacteria. SCIENCE ADVANCES 2021; 7:7/7/eabe1870. [PMID: 33568484 PMCID: PMC7875522 DOI: 10.1126/sciadv.abe1870] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/23/2020] [Indexed: 05/24/2023]
Abstract
The electric wires of cable bacteria possibly support a unique respiration mode with a few oxygen-reducing cells flaring off electrons, while oxidation of the electron donor and the associated energy conservation and growth is allocated to other cells not exposed to oxygen. Cable bacteria are centimeter-long, multicellular, filamentous Desulfobulbaceae that transport electrons across oxic-anoxic interfaces in aquatic sediments. From observed distortions of the oxic-anoxic interface, we derived oxygen consumption rates of individual cable bacteria and found biomass-specific rates of unheard magnitude in biology. Tightly controlled behavior, possibly involving intercellular electrical signaling, was found to generally keep <10% of individual filaments exposed to oxygen. The results strengthen the hypothesis that cable bacteria indeed have evolved an exceptional way to take the full energetic advantages of aerobic respiration and let >90% of the cells metabolize in the convenient absence of oxidative stress.
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Affiliation(s)
- Stefano Scilipoti
- Center for Electromicrobiology, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark.
| | - Klaus Koren
- Aarhus University Center for Water Technology, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Nils Risgaard-Petersen
- Center for Electromicrobiology, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Andreas Schramm
- Center for Electromicrobiology, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Lars Peter Nielsen
- Center for Electromicrobiology, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark.
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Intestinal bacteria are potential biomarkers and therapeutic targets for gastric cancer. Microb Pathog 2021; 151:104747. [PMID: 33484807 DOI: 10.1016/j.micpath.2021.104747] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/13/2022]
Abstract
The diagnostic and therapeutic role of intestinal microbiota in gastric carcinogenesis remains unclear. In this study, feces from gastric cancer patients and healthy people were sequenced for microbiota analysis, and the correlation between fecal bacteria and the occurrence of gastric cancer was explored. The β-diversity results showed that microbial compositions varied between gastric cancer patients and healthy people. Interestingly, the dissection of microbial structure revealed that all facultative anaerobic genera with relatively high abundances expanded significantly in gastric cancer patients. The succeeding correlation analysis demonstrated a distorted interaction of intestinal bacteria in gastric cancer. The application of some differential bacteria, Desulfovibrio, Escherichia, Faecalibacterium or Oscillospira, as biomarkers to predict gastric cancer could all reach an accuracy of 0.900 or above. The shift in Desulfovibrio was specifically verified by qPCR in newly collected fecal samples, and the patients with stage IV gastric cancer were identified to have significantly more Desulfovibrio than those with stage I, II and III gastric cancer. The possible role of Desulfovibrio in gastric cancer was assessed with H2S-treated HT-29 cells, and the results showed that H2S induced NO, IL-1β and IL-18 production, which is important for inflammation promotion and can be delivered through the bloodstream. This study suggests a correlation of intestinal microbiota and the development of gastric cancer.
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Khademian M, Imlay JA. Do reactive oxygen species or does oxygen itself confer obligate anaerobiosis? The case of Bacteroides thetaiotaomicron. Mol Microbiol 2020; 114:333-347. [PMID: 32301184 DOI: 10.1111/mmi.14516] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 02/06/2023]
Abstract
Bacteroides thetaiotaomicron was examined to determine whether its obligate anaerobiosis is imposed by endogenous reactive oxygen species or by molecular oxygen itself. Previous analyses established that aerated B. thetaiotaomicron loses some enzyme activities due to a high rate of endogenous superoxide formation. However, the present study establishes that another key step in central metabolism is poisoned by molecular oxygen itself. Pyruvate dissimilation was shown to depend upon two enzymes, pyruvate:formate lyase (PFL) and pyruvate:ferredoxin oxidoreductase (PFOR), that lose activity upon aeration. PFL is a glycyl-radical enzyme whose vulnerability to oxygen is already understood. The rate of PFOR damage was unaffected by the level of superoxide or peroxide, showing that molecular oxygen itself is the culprit. The cell cannot repair PFOR, which amplifies the impact of damage. The rates of PFOR and fumarase inactivation are similar, suggesting that superoxide dismutase is calibrated so the oxygen- and superoxide-sensitive enzymes are equally sensitive to aeration. The physiological purpose of PFL and PFOR is to degrade pyruvate without disrupting the redox balance, and they do so using catalytic mechanisms that are intrinsically vulnerable to oxygen. In this way, the anaerobic excellence and oxygen sensitivity of B. thetaiotaomicron are two sides of the same coin.
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Affiliation(s)
- Maryam Khademian
- Department of Microbiology, University of Illinois, Urbana, IL, USA
| | - James A Imlay
- Department of Microbiology, University of Illinois, Urbana, IL, USA
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" Candidatus Desulfobulbus rimicarensis," an Uncultivated Deltaproteobacterial Epibiont from the Deep-Sea Hydrothermal Vent Shrimp Rimicaris exoculata. Appl Environ Microbiol 2020; 86:AEM.02549-19. [PMID: 32060020 PMCID: PMC7117923 DOI: 10.1128/aem.02549-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/26/2020] [Indexed: 02/03/2023] Open
Abstract
The shrimp Rimicaris exoculata represents the dominant faunal biomass at many deep-sea hydrothermal vent ecosystems along the Mid-Atlantic Ridge. This organism harbors dense bacterial epibiont communities in its enlarged cephalothoracic chamber that play an important nutritional role. Deltaproteobacteria are ubiquitous in epibiotic communities of R. exoculata, and their functional roles as epibionts are based solely on the presence of functional genes. Here, we describe “Candidatus Desulfobulbus rimicarensis,” an uncultivated deltaproteobacterial epibiont. Compared to campylobacterial and gammaproteobacterial epibionts of R. exoculata, this bacterium possessed unique metabolic pathways, such as the Wood-Ljungdahl pathway, as well as sulfur disproportionation and nitrogen fixation pathways. Furthermore, this epibiont can be distinguished from closely related free-living Desulfobulbus strains by its reduced genetic content and potential loss of functions, suggesting unique adaptations to the shrimp host. This study is a genomic and transcriptomic analysis of a deltaproteobacterial epibiont and largely expands the understanding of its metabolism and adaptation to the R. exoculata host. The deep-sea hydrothermal vent shrimp Rimicaris exoculata largely depends on a dense epibiotic chemoautotrophic bacterial community within its enlarged cephalothoracic chamber. However, our understanding of shrimp-bacterium interactions is limited. In this report, we focused on the deltaproteobacterial epibiont of R. exoculata from the relatively unexplored South Mid-Atlantic Ridge. A nearly complete genome of a Deltaproteobacteria epibiont was binned from the assembled metagenome. Whole-genome phylogenetic analysis reveals that it is affiliated with the genus Desulfobulbus, representing a potential novel species for which the name “Candidatus Desulfobulbus rimicarensis” is proposed. Genomic and transcriptomic analyses reveal that this bacterium utilizes the Wood-Ljungdahl pathway for carbon assimilation and harvests energy via sulfur disproportionation, which is significantly different from other shrimp epibionts. Additionally, this epibiont has putative nitrogen fixation activity, but it is extremely active in directly taking up ammonia and urea from the host or vent environments. Moreover, the epibiont could be distinguished from its free-living relatives by various features, such as the lack of chemotaxis and motility traits, a dramatic reduction in biosynthesis genes for capsular and extracellular polysaccharides, enrichment of genes required for carbon fixation and sulfur metabolism, and resistance to environmental toxins. Our study highlights the unique role and symbiotic adaptation of Deltaproteobacteria in deep-sea hydrothermal vent shrimps. IMPORTANCE The shrimp Rimicaris exoculata represents the dominant faunal biomass at many deep-sea hydrothermal vent ecosystems along the Mid-Atlantic Ridge. This organism harbors dense bacterial epibiont communities in its enlarged cephalothoracic chamber that play an important nutritional role. Deltaproteobacteria are ubiquitous in epibiotic communities of R. exoculata, and their functional roles as epibionts are based solely on the presence of functional genes. Here, we describe “Candidatus Desulfobulbus rimicarensis,” an uncultivated deltaproteobacterial epibiont. Compared to campylobacterial and gammaproteobacterial epibionts of R. exoculata, this bacterium possessed unique metabolic pathways, such as the Wood-Ljungdahl pathway, as well as sulfur disproportionation and nitrogen fixation pathways. Furthermore, this epibiont can be distinguished from closely related free-living Desulfobulbus strains by its reduced genetic content and potential loss of functions, suggesting unique adaptations to the shrimp host. This study is a genomic and transcriptomic analysis of a deltaproteobacterial epibiont and largely expands the understanding of its metabolism and adaptation to the R. exoculata host.
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Zhang Y, Liu Y, Li J, Xing T, Jiang Y, Zhang L, Gao F. Dietary resistant starch modifies the composition and function of caecal microbiota of broilers. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:1274-1284. [PMID: 31721238 DOI: 10.1002/jsfa.10139] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Diet plays an important role in shaping the composition of gut microbiota. Starch is the main source of carbohydrates in diets of broilers. This study investigated the effects of dietary corn starch and resistant starch on composition and function of caecal microbiota of broilers. A total of 320, 1-day-old male Arbor Acres broiler chicks were randomly assigned into five groups including normal corn-soybean (NC) diet, corn starch (CS) diet group, 4%, 8% and 12% resistant starch (RS) diet groups. The caecal contents of 42-day old broilers were sampled and microbiota community was analysed with 16S rRNA gene sequences. RESULTS The CS group increased the abundances of Bilophila, Eggerthella, Olsenella and Sellimonas and decreased proportion of Akkermansia, Eisenbergiella, Oscillospira, Ruminococcaceae NK4A214 group and Synergistes in the caecum of birds compared to the NC group. However, the birds from RS groups had higher abundances of Anaerofilum, Bacteroides, Desulfovibrio and Parasutterella and lower abundances of Alistipes, Bilophila, Christensenellaceae R-7 group, Eggerthella and Ruminiclostridium 1 than the CS group. Functional prediction of these changes in microbiota revealed that the CS diet drove caecal microbiota that were more inclined to utilize carbohydrates through glycolysis/gluconeogenesis metabolism, while the 8%RS and 12%RS diets depleted microbial glycolysis/gluconeogenesis and amino acids metabolism. CONCLUSION Dietary CS and RS alter the microbial composition and diversity, and modulate the metabolic pathways of microbial metabolism in caecum of broilers, which may further affect nutrient utilization and hindgut health of the host. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Yingying Zhang
- College of Animal Science and Technology, Jiangsu Provincial Key Laboratory of Animal Origin Food Production and Safety Guarantee, Jiangsu Provincial Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Joint International Research Laboratory of Animal Health and Food Safety, National Experimental Teaching Demonstration Centre of Animal Science, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yingsen Liu
- College of Animal Science and Technology, Jiangsu Provincial Key Laboratory of Animal Origin Food Production and Safety Guarantee, Jiangsu Provincial Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Joint International Research Laboratory of Animal Health and Food Safety, National Experimental Teaching Demonstration Centre of Animal Science, Nanjing Agricultural University, Nanjing, P. R. China
| | - Jiaolong Li
- College of Animal Science and Technology, Jiangsu Provincial Key Laboratory of Animal Origin Food Production and Safety Guarantee, Jiangsu Provincial Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Joint International Research Laboratory of Animal Health and Food Safety, National Experimental Teaching Demonstration Centre of Animal Science, Nanjing Agricultural University, Nanjing, P. R. China
| | - Tong Xing
- College of Animal Science and Technology, Jiangsu Provincial Key Laboratory of Animal Origin Food Production and Safety Guarantee, Jiangsu Provincial Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Joint International Research Laboratory of Animal Health and Food Safety, National Experimental Teaching Demonstration Centre of Animal Science, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yun Jiang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, P. R. China
| | - Lin Zhang
- College of Animal Science and Technology, Jiangsu Provincial Key Laboratory of Animal Origin Food Production and Safety Guarantee, Jiangsu Provincial Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Joint International Research Laboratory of Animal Health and Food Safety, National Experimental Teaching Demonstration Centre of Animal Science, Nanjing Agricultural University, Nanjing, P. R. China
| | - Feng Gao
- College of Animal Science and Technology, Jiangsu Provincial Key Laboratory of Animal Origin Food Production and Safety Guarantee, Jiangsu Provincial Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Joint International Research Laboratory of Animal Health and Food Safety, National Experimental Teaching Demonstration Centre of Animal Science, Nanjing Agricultural University, Nanjing, P. R. China
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Increasing oxygen deficiency changes rare and moderately abundant bacterial communities in coastal soft sediments. Sci Rep 2019; 9:16341. [PMID: 31704947 PMCID: PMC6841974 DOI: 10.1038/s41598-019-51432-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/25/2019] [Indexed: 11/20/2022] Open
Abstract
Coastal hypoxia is a major environmental problem worldwide. Hypoxia-induced changes in sediment bacterial communities harm marine ecosystems and alter biogeochemical cycles. Nevertheless, the resistance of sediment bacterial communities to hypoxic stress is unknown. We investigated changes in bacterial communities during hypoxic-anoxic disturbance by artificially inducing oxygen deficiency to the seafloor for 0, 3, 7, and 48 days, with subsequent molecular biological analyses. We further investigated relationships between bacterial communities, benthic macrofauna and nutrient effluxes across the sediment-water-interface during hypoxic-anoxic stress, considering differentially abundant operational taxonomic units (OTUs). The composition of the moderately abundant OTUs changed significantly after seven days of oxygen deficiency, while the abundant and rare OTUs first changed after 48 days. High bacterial diversity maintained the resistance of the communities during oxygen deficiency until it dropped after 48 days, likely due to anoxia-induced loss of macrofaunal diversity and bioturbation. Nutrient fluxes, especially ammonium, correlated positively with the moderate and rare OTUs, including potential sulfate reducers. Correlations may reflect bacteria-mediated nutrient effluxes that accelerate eutrophication. The study suggests that even slightly higher bottom-water oxygen concentrations, which could sustain macrofaunal bioturbation, enable bacterial communities to resist large compositional changes and decrease the harmful consequences of hypoxia in marine ecosystems.
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29
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Cable bacteria, living electrical conduits in the microbial world. Proc Natl Acad Sci U S A 2019; 116:18759-18761. [PMID: 31501332 DOI: 10.1073/pnas.1913413116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Murray AM, Maillard J, Jin B, Broholm MM, Holliger C, Rolle M. A modeling approach integrating microbial activity, mass transfer, and geochemical processes to interpret biological assays: An example for PCE degradation in a multi-phase batch setup. WATER RESEARCH 2019; 160:484-496. [PMID: 31177078 DOI: 10.1016/j.watres.2019.05.087] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/22/2019] [Accepted: 05/25/2019] [Indexed: 06/09/2023]
Abstract
The rate at which organic contaminants can be degraded in aquatic environments is not only dependent upon specific degrading bacteria, but also upon the composition of the microbial community, mass transfer of the contaminant, and abiotic processes that occur in the environment. In this study, we present three-phase batch experiments of tetrachloroethene (PCE) degradation by a consortium of organohalide-respiring bacteria, cultivated alone or in communities with iron- and/or sulfate-reducers. We developed a modeling approach to quantitatively evaluate the experimental results, comprised of chemical and biomolecular time series data. The model utilizes the IPhreeqc module to couple multi-phase mass transfer between gaseous, organic and aqueous phases with microbial and aquatic geochemical processes described using the geochemical code PHREEQC. The proposed approach is able to capture the contaminant degradation, the microbial population dynamics, the effects of multi-phase kinetic mass transfer and sample removal, and the geochemical reactions occurring in the aqueous phase. The model demonstrates the importance of aqueous speciation and abiotic reactions on the bioavailability of the substrates. The model-based interpretation allowed us to quantify the reaction kinetics of the different bacterial guilds. The model further revealed that the inclusion of sulfate-reducing bacteria lowers the rate of PCE degradation and that this effect is moderated in the presence of iron-reducing bacteria.
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Affiliation(s)
- Alexandra Marie Murray
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, ENAC-IIE, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Biao Jin
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Science, China
| | - Mette M Broholm
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, ENAC-IIE, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Massimo Rolle
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark.
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31
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Purkamo L, Kietäväinen R, Miettinen H, Sohlberg E, Kukkonen I, Itävaara M, Bomberg M. Diversity and functionality of archaeal, bacterial and fungal communities in deep Archaean bedrock groundwater. FEMS Microbiol Ecol 2019; 94:5035813. [PMID: 29893836 DOI: 10.1093/femsec/fiy116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/08/2018] [Indexed: 01/19/2023] Open
Abstract
The diversity and metabolic functions of deep subsurface ecosystems remain relatively unexplored. Microbial communities in previously studied deep subsurface sites of the Fennoscandian Shield are distinctive to each site. Thus, we hypothesized that the microbial communities of the deep Archaean bedrock fracture aquifer in Romuvaara, northern Finland, differ both in community composition and metabolic functionality from the other sites in the Fennoscandian Shield. We characterized the composition, functionality and substrate preferences of the microbial communities at different depths in a 600 m deep borehole. In contrast to other Fennoscandian deep biosphere communities studied to date, iron-oxidizing Gallionella dominated the bacterial communities, while methanogenic and ammonia-oxidizing archaea were the most prominent archaea, and a diverse fungal community was also detected. Potential for methane cycling and sulfate and nitrate reduction was confirmed by detection of the functional genes of these metabolic pathways. Organotrophs were less abundant, although carbohydrates were the most preferred of the tested substrates. The microbial communities shared features with those detected from other deep groundwaters with similar geochemistry, but the majority of taxa distinctive to Romuvaara are different from the taxa previously detected in saline deep groundwater in the Fennoscandian Shield, most likely because of the differences in water chemistry.
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Affiliation(s)
- Lotta Purkamo
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Riikka Kietäväinen
- Geological Survey of Finland (GTK), Betonimiehenkuja 4, 02151 Espoo, Finland
| | - Hanna Miettinen
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Elina Sohlberg
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Ilmo Kukkonen
- Geological Survey of Finland (GTK), Betonimiehenkuja 4, 02151 Espoo, Finland
| | - Merja Itävaara
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Malin Bomberg
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
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Baffert C, Kpebe A, Avilan L, Brugna M. Hydrogenases and H 2 metabolism in sulfate-reducing bacteria of the Desulfovibrio genus. Adv Microb Physiol 2019; 74:143-189. [PMID: 31126530 DOI: 10.1016/bs.ampbs.2019.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Hydrogen metabolism plays a central role in sulfate-reducing bacteria of the Desulfovibrio genus and is based on hydrogenases that catalyze the reversible conversion of protons into dihydrogen. These metabolically versatile microorganisms possess a complex hydrogenase system composed of several enzymes of both [FeFe]- and [NiFe]-type that can vary considerably from one Desulfovibrio species to another. This review covers the molecular and physiological aspects of hydrogenases and H2 metabolism in Desulfovibrio but focuses particularly on our model bacterium Desulfovibrio fructosovorans. The search of hydrogenase genes in more than 30 sequenced genomes provides an overview of the distribution of these enzymes in Desulfovibrio. Our discussion will consider the significance of the involvement of electron-bifurcation in H2 metabolism.
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Affiliation(s)
- Carole Baffert
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Arlette Kpebe
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Luisana Avilan
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Myriam Brugna
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
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Environmental filtering determines family-level structure of sulfate-reducing microbial communities in subsurface marine sediments. ISME JOURNAL 2019; 13:1920-1932. [PMID: 30894690 DOI: 10.1038/s41396-019-0387-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/22/2019] [Accepted: 02/28/2019] [Indexed: 01/09/2023]
Abstract
Recent work has shown that subsurface microbial communities assemble by selective survival of surface community members during sediment burial, but it remains unclear to what extent the compositions of the subsurface communities are a product of their founding population at the sediment surface or of the changing geochemical conditions during burial. Here we investigate this question for communities of sulfate-reducing microorganisms (SRMs). We collected marine sediment samples from the upper 3-5 m at four geochemically contrasting sites in the Skagerrak and Baltic Sea and measured SRM abundance (quantitative PCR of dsrB), metabolic activity (radiotracer rate measurements), and community composition (Illumina sequencing of dsrB amplicons). These data showed that SRM abundance, richness, and phylogenetic clustering as determined by the nearest taxon index peaked below the bioturbation zone and above the depth of sulfate depletion. Minimum cell-specific rates of sulfate reduction did not vary substantially between sites. SRM communities at different sites were best distinguished based on their composition of amplicon sequence variants (ASVs), while communities in different geochemical zones were best distinguished based on their composition of SRM families. This demonstrates environmental filtering of SRM communities in sediment while a site-specific fingerprint of the founding community is retained.
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Formate-removing inoculum dominated by Methanobacterium congolense supports succinate production from crude glycerol fermentation. J Ind Microbiol Biotechnol 2019; 46:625-634. [PMID: 30783892 DOI: 10.1007/s10295-019-02154-w] [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: 08/24/2018] [Accepted: 02/12/2019] [Indexed: 10/27/2022]
Abstract
We developed a formate-removing methanogenic inoculum (FRI) to facilitate succinate production from crude glycerol by Escherichia coli. FRI converted formate to methane, thereby enabling glycerol fermentation without additional electron acceptors under neutral pH. FRI was selectively enriched from sludge from the anaerobic digester of the Seonam sewage treatment plant (Seoul); this process was assessed via Illumina sequencing and scanning electron microscopy imaging. Methanobacterium congolense species occupied only 0.3% of the archaea community in the sludge and was enriched to 99.5% in complete FRI, wherein succinate-degrading bacteria were successfully eliminated. Co-culture with FRI improved glycerol fermentation and yielded 7.3 mM succinate from 28.7 mM crude glycerol, whereby FRI completely converted formate into methane. This study is the first to demonstrate methane production by M. congolense species, using formate. M. congolense-dominated FRI can serve as a renewable facilitator of waste feedstock fermentation and enable the production of commercially important compounds.
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Labrado AL, Brunner B, Bernasconi SM, Peckmann J. Formation of Large Native Sulfur Deposits Does Not Require Molecular Oxygen. Front Microbiol 2019; 10:24. [PMID: 30740094 PMCID: PMC6355691 DOI: 10.3389/fmicb.2019.00024] [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: 09/28/2018] [Accepted: 01/09/2019] [Indexed: 01/05/2023] Open
Abstract
Large native (i.e., elemental) sulfur deposits can be part of caprock assemblages found on top of or in lateral position to salt diapirs and as stratabound mineralization in gypsum and anhydrite lithologies. Native sulfur is formed when hydrocarbons come in contact with sulfate minerals in presence of liquid water. The prevailing model for native sulfur formation in such settings is that sulfide produced by sulfate-reducing bacteria is oxidized to zero-valent sulfur in presence of molecular oxygen (O2). Although possible, such a scenario is problematic because: (1) exposure to oxygen would drastically decrease growth of microbial sulfate-reducing organisms, thereby slowing down sulfide production; (2) on geologic timescales, excess supply with oxygen would convert sulfide into sulfate rather than native sulfur; and (3) to produce large native sulfur deposits, enormous amounts of oxygenated water would need to be brought in close proximity to environments in which ample hydrocarbon supply sustains sulfate reduction. However, sulfur stable isotope data from native sulfur deposits emplaced at a stage after the formation of the host rocks indicate that the sulfur was formed in a setting with little solute exchange with the ambient environment and little supply of dissolved oxygen. We deduce that there must be a process for the formation of native sulfur in absence of an external oxidant for sulfide. We hypothesize that in systems with little solute exchange, sulfate-reducing organisms, possibly in cooperation with other anaerobic microbial partners, drive the formation of native sulfur deposits. In order to cope with sulfide stress, microbes may shift from harmful sulfide production to non-hazardous native sulfur production. We propose four possible mechanisms as a means to form native sulfur: (1) a modified sulfate reduction process that produces sulfur compounds with an intermediate oxidation state, (2) coupling of sulfide oxidation to methanogenesis that utilizes methylated compounds, acetate or carbon dioxide, (3) ammonium oxidation coupled to sulfate reduction, and (4) sulfur comproportionation of sulfate and sulfide. We show these reactions are thermodynamically favorable and especially useful in environments with multiple stressors, such as salt and dissolved sulfide, and provide evidence that microbial species functioning in such environments produce native sulfur. Integrating these insights, we argue that microbes may form large native sulfur deposits in absence of light and external oxidants such as O2, nitrate, and metal oxides. The existence of such a process would not only explain enigmatic occurrences of native sulfur in the geologic record, but also provide an explanation for cryptic sulfur and carbon cycling beneath the seabed.
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Affiliation(s)
- Amanda L. Labrado
- Department of Geological Sciences, The University of Texas at El Paso, El Paso, TX, United States
| | - Benjamin Brunner
- Department of Geological Sciences, The University of Texas at El Paso, El Paso, TX, United States
| | | | - Jörn Peckmann
- Centrum für Erdsystemforschung und Nachhaltigkeit, Universität Hamburg, Hamburg, Germany
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Mori F, Umezawa Y, Kondo R, Wada M. Dynamics of Sulfate-Reducing Bacteria Community Structure in Surface Sediment of a Seasonally Hypoxic Enclosed Bay. Microbes Environ 2018; 33:378-384. [PMID: 30449831 PMCID: PMC6308007 DOI: 10.1264/jsme2.me18092] [Citation(s) in RCA: 4] [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
We herein report on the dynamics of a sulfate-reducing bacteria (SRB) community structure in the surface sediment of a seasonally hypoxic enclosed bay for two consecutive years (2012 and 2013). The uppermost (0–5 mm) and subsurface (5–10 mm) layers of sediment were examined with a terminal-restriction fragment length polymorphism (T-RFLP) analysis based on the dissimilatory sulfite reductase (dsrA) gene. The SRB community significantly differed between the two sediment layers over the sampling period. This difference was mainly attributed to operational taxonomic units (OTUs) that were unique to either of the sediment layers. However, nearly 70% of total OTUs were shared between the two layers, with a few predominating. Therefore, no significant shift was observed in the SRB community structure under varying dissolved oxygen (DO) conditions in bottom water overlying the sediment surface. An additional analysis of 16S rRNA gene amplicon sequences, conducted for three uppermost sediment samples (July, August, and September in 2012), revealed that Desulfococcus, a member of SRB with high tolerance to oxygen, was the predominant Deltaproteobacteria across the uppermost sediment samples. Based on the predominance of shared OTUs across the SRB community in the sediment (0–10 mm) regardless of bottom-water DO, some SRB that are physiologically tolerant of a wide range of DO conditions may have dominated and masked changes in responsive SRB to DO concentrations. These results suggest that the SRB community structure in the enclosed bay became stable under repeated cycles of seasonal hypoxia, but may be compromised if the severity of hypoxia increases in the future.
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Affiliation(s)
- Fumiaki Mori
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University
| | - Yu Umezawa
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University
| | - Ryuji Kondo
- Department of Marine Science and Technology, Fukui Prefectural University
| | - Minoru Wada
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University
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Schoeffler M, Gaudin AL, Ramel F, Valette O, Denis Y, Hania WB, Hirschler-Réa A, Dolla A. Growth of an anaerobic sulfate-reducing bacterium sustained by oxygen respiratory energy conservation after O 2 -driven experimental evolution. Environ Microbiol 2018; 21:360-373. [PMID: 30394641 DOI: 10.1111/1462-2920.14466] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 11/30/2022]
Abstract
Desulfovibrio species are representatives of microorganisms at the boundary between anaerobic and aerobic lifestyles, since they contain the enzymatic systems required for both sulfate and oxygen reduction. However, the latter has been shown to be solely a protective mechanism. By implementing the oxygen-driven experimental evolution of Desulfovibrio vulgaris Hildenborough, we have obtained strains that have evolved to grow with energy derived from oxidative phosphorylation linked to oxygen reduction. We show that a few mutations are sufficient for the emergence of this phenotype and reveal two routes of evolution primarily involving either inactivation or overexpression of the gene encoding heterodisulfide reductase. We propose that the oxygen respiration for energy conservation that sustains the growth of the O2 -evolved strains is associated with a rearrangement of metabolite fluxes, especially NAD+ /NADH, leading to an optimized O2 reduction. These evolved strains are the first sulfate-reducing bacteria that exhibit a demonstrated oxygen respiratory process that enables growth.
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Affiliation(s)
- Marine Schoeffler
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Anne-Laure Gaudin
- Aix Marseille Université, CNRS, LCB, Marseille, France.,GERME SA, Technopôle de Château Gombert, Marseille, France
| | - Fanny Ramel
- Aix Marseille Université, CNRS, LCB, Marseille, France
| | - Odile Valette
- Aix Marseille Université, CNRS, LCB, Marseille, France
| | - Yann Denis
- Aix Marseille Université, CNRS, IMM, Marseille, France
| | - Wagdi Ben Hania
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Agnès Hirschler-Réa
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Alain Dolla
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
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38
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Ledón-Rettig CC, Moczek AP, Ragsdale EJ. Diplogastrellus nematodes are sexually transmitted mutualists that alter the bacterial and fungal communities of their beetle host. Proc Natl Acad Sci U S A 2018; 115:10696-10701. [PMID: 30275294 PMCID: PMC6196496 DOI: 10.1073/pnas.1809606115] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A recent accumulation of studies has demonstrated that nongenetic, maternally transmitted factors are often critical to the health and development of offspring and can therefore play a role in ecological and evolutionary processes. In particular, microorganisms such as bacteria have been championed as heritable, symbiotic partners capable of conferring fitness benefits to their hosts. At the same time, parents may also pass various nonmicrobial organisms to their offspring, yet the roles of such organisms in shaping the developmental environment of their hosts remain largely unexplored. Here, we show that the nematode Diplogastrellus monhysteroides is transgenerationally inherited and sexually transmitted by the dung beetle Onthophagus taurus By manipulating artificial chambers in which beetle offspring develop, we demonstrate that the presence of D. monhysteroides nematodes enhances the growth of beetle offspring, empirically challenging the paradigm that nematodes are merely commensal or even detrimental to their insect hosts. Finally, our research presents a compelling mechanism whereby the nematodes influence the health of beetle larvae: D. monhysteroides nematodes engineer the bacterial and fungal communities that also inhabit the beetle developmental chambers, including specific taxa known to be involved in biomass degradation, possibly allowing larval beetles better access to their otherwise recalcitrant, plant-based diet. Thus, our findings illustrate that nongenetic inheritance can include intermediately sized organisms that live and proliferate in close association with, and in certain cases enhance, the development of their hosts' offspring.
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Affiliation(s)
| | - Armin P Moczek
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Erik J Ragsdale
- Department of Biology, Indiana University, Bloomington, IN 47405
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Liu W, Long Y, Fang Y, Ying L, Shen D. A novel aerobic sulfate reduction process in landfill mineralized refuse. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:174-181. [PMID: 29751300 DOI: 10.1016/j.scitotenv.2018.04.304] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/05/2018] [Accepted: 04/23/2018] [Indexed: 06/08/2023]
Abstract
It is thought that mineralized refuse could be excavated from almost-full landfill sites to provide space for the increasing burden of municipal solid waste. When excavating, however, the H2S emissions from the mineralized waste need to be considered carefully. In an attempt to understand how H2S emissions might change during this excavation process, we carried out a series of tests, including exposing anaerobic mineralized refuse to oxygen, isolating and determining possible functional bacteria, and characterizing the electron donors and/or acceptors. The results showed that H2S would be released when landfill mineralized refuse was exposed to oxygen (O2), and could reach concentrations of 6 mg m-3, which was 3 times the concentrations of H2S released from anaerobic mineralized refuse. Sulfur-metabolized microorganisms accounted for only 0.5% of the microbial functional bacteria (MFB) derived from the mineralized refuse when exposed to O2 for 60 days, and SRB were not present. The MFB maintained H2S production by aerobic sulfate reduction using SO42- and S2O32- as electron acceptors, and sulfate-reducing rates of 16% and 55%, respectively, were achieved. Lactate and S2O32- were the preferred electron donor and acceptor, respectively. By enhancing the carbon source and electron transfer, MFB may undergo strong aerobic sulfate reduction even at low abundances of sulfur-metabolized microorganisms.
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Affiliation(s)
- Weijia Liu
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Yuyang Long
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China.
| | - Yuan Fang
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Luyao Ying
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Dongsheng Shen
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
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Sousa JR, Silveira CM, Fontes P, Roma-Rodrigues C, Fernandes AR, Van Driessche G, Devreese B, Moura I, Moura JJ, Almeida MG. Understanding the response of Desulfovibrio desulfuricans ATCC 27774 to the electron acceptors nitrate and sulfate - biosynthetic costs modulate substrate selection. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1455-1469. [DOI: 10.1016/j.bbapap.2017.07.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/12/2017] [Accepted: 07/21/2017] [Indexed: 11/27/2022]
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Alonso-Pernas P, Bartram S, Arias-Cordero EM, Novoselov AL, Halty-deLeon L, Shao Y, Boland W. In Vivo Isotopic Labeling of Symbiotic Bacteria Involved in Cellulose Degradation and Nitrogen Recycling within the Gut of the Forest Cockchafer ( Melolontha hippocastani). Front Microbiol 2017; 8:1970. [PMID: 29075241 PMCID: PMC5643479 DOI: 10.3389/fmicb.2017.01970] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/25/2017] [Indexed: 11/17/2022] Open
Abstract
The guts of insects harbor symbiotic bacterial communities. However, due to their complexity, it is challenging to relate a specific symbiotic phylotype to its corresponding function. In the present study, we focused on the forest cockchafer (Melolontha hippocastani), a phytophagous insect with a dual life cycle, consisting of a root-feeding larval stage and a leaf-feeding adult stage. By combining in vivo stable isotope probing (SIP) with 13C cellulose and 15N urea as trophic links, with Illumina MiSeq (Illumina-SIP), we unraveled bacterial networks processing recalcitrant dietary components and recycling nitrogenous waste. The bacterial communities behind these processes change between larval and adult stages. In 13C cellulose-fed insects, the bacterial families Lachnospiraceae and Enterobacteriaceae were isotopically labeled in larvae and adults, respectively. In 15N urea-fed insects, the genera Burkholderia and Parabacteroides were isotopically labeled in larvae and adults, respectively. Additionally, the PICRUSt-predicted metagenome suggested a possible ability to degrade hemicellulose and to produce amino acids of, respectively, 13C cellulose- and 15N urea labeled bacteria. The incorporation of 15N from ingested urea back into the insect body was confirmed, in larvae and adults, by isotope ratio mass spectrometry (IRMS). Besides highlighting key bacterial symbionts of the gut of M. hippocastani, this study provides example on how Illumina-SIP with multiple trophic links can be used to target microorganisms embracing different roles within an environment.
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Affiliation(s)
- Pol Alonso-Pernas
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Stefan Bartram
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Erika M Arias-Cordero
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Alexey L Novoselov
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Lorena Halty-deLeon
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Yongqi Shao
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Wilhelm Boland
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
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Wang C, Liu S, Zhang Y, Liu B, Zeng L, He F, Zhou Q, Wu Z. Effects of Planted Versus Naturally Growing Vallisneria natans on the Sediment Microbial Community in West Lake, China. MICROBIAL ECOLOGY 2017; 74:278-288. [PMID: 28255685 DOI: 10.1007/s00248-017-0951-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/13/2017] [Indexed: 06/06/2023]
Abstract
Submerged macrophytes play an important role in aquatic ecosystems, which has led to an increase in studies on vegetation recovery in polluted lakes from which submerged macrophytes have disappeared. The comparison of microbial communities in sediment cloned with planted and naturally growing submerged macrophytes is an interesting but rarely studied topic. In this investigation, Maojiabu and Xilihu, two adjacent sublakes of West Lake (Hangzhou, China), were selected as aquatic areas with planted and naturally growing macrophytes, respectively. Sediment samples from sites with/without Vallisneria natans were collected from both sublakes. The results showed that sediment total nitrogen and organic matter were significantly lower in the plant-covered sites than that in the non-plant sites in Maojiabu. Additionally, the sediment microbial community characterized by 16S ribosomal RNA (rRNA) sequencing differed more significantly for Maojiabu than for Xilihu. The relative abundances of microbes involved in C, N, and S elemental cycling were significantly higher in the sediments with plants than in those without. Results from both fatty acid methyl ester analysis and 16S rRNA sequencing indicated that vegetation significantly influenced the sulfate-reducing bacteria (SRB). Thus, the gene copies and composition of SRB were explored further. The relative gene abundance of SRB was 66% higher with natural vegetation colonization but was not influenced by artificial colonization. An increase in dominant SRB members from the families Syntrophobacteraceae and Thermodesulfovibrionaceae contributed to the increase of total SRB. Thus, macrophyte planting influences sediment nutrient levels and microbial community more than natural growth does, whereas the latter is more beneficial to sediment SRB.
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Affiliation(s)
- Chuan Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, 430072, China
- University of Chinese Academy of Sciences, 19 A Yuquan Rd., Shijingshan District, Beijing, 100049, China
| | - Shuangyuan Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, 430072, China
- University of Chinese Academy of Sciences, 19 A Yuquan Rd., Shijingshan District, Beijing, 100049, China
| | - Yi Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, 430072, China
| | - Biyun Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, 430072, China
| | - Lei Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, 430072, China
- University of Chinese Academy of Sciences, 19 A Yuquan Rd., Shijingshan District, Beijing, 100049, China
| | - Feng He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, 430072, China
| | - Qiaohong Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, 430072, China.
| | - Zhenbin Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, 430072, China
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43
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Selection for novel, acid-tolerant Desulfovibrio spp. from a closed Transbaikal mine site in a temporal pH-gradient bioreactor. Antonie van Leeuwenhoek 2017; 110:1669-1679. [DOI: 10.1007/s10482-017-0917-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 07/20/2017] [Indexed: 10/19/2022]
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Selvaraj H, Chandrasekaran K, Murugan R, Sundaram M. An integrated biological and electrochemical process for recovery of sulfur from an industrial effluent contaminated pond water and its preliminary application in high performance battery. Sep Purif Technol 2017. [DOI: 10.1016/j.seppur.2017.01.069] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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45
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Zhang P, He Z, Van Nostrand JD, Qin Y, Deng Y, Wu L, Tu Q, Wang J, Schadt CW, W Fields M, Hazen TC, Arkin AP, Stahl DA, Zhou J. Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:3609-3620. [PMID: 28300407 DOI: 10.1021/acs.est.6b02980] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
To further understand the diversity and dynamics of SRB in response to substrate amendment, we sequenced genes coding for the dissimilatory sulfite reductase (dsrA) in groundwater samples collected after an emulsified vegetable oil (EVO) amendment, which sustained U(VI)-reducing conditions for one year in a fast-flowing aquifer. EVO amendment significantly altered the composition of groundwater SRB communities. Sequences having no closely related-described species dominated (80%) the indigenous SRB communities in nonamended wells. After EVO amendment, Desulfococcus, Desulfobacterium, and Desulfovibrio, known for long-chain-fatty-acid, short-chain-fatty-acid and H2 oxidation and U(VI) reduction, became dominant accounting for 7 ± 2%, 21 ± 8%, and 55 ± 8% of the SRB communities, respectively. Succession of these SRB at different bioactivity stages based on redox substrates/products (acetate, SO4-2, U(VI), NO3-, Fe(II), and Mn(II)) was observed. Desulfovibrio and Desulfococcus dominated SRB communities at 4-31 days, whereas Desulfobacterium became dominant at 80-140 days. By the end of the experiment (day 269), the abundance of these SRB decreased but the overall diversity of groundwater SRB was still higher than non-EVO controls. Up to 62% of the SRB community changes could be explained by groundwater geochemical variables, including those redox substrates/products. A significant (P < 0.001) correlation was observed between groundwater U(VI) concentrations and Desulfovibrio abundance. Our results showed that the members of SRB and their dynamics were correlated significantly with slow EVO biodegradation, electron donor production and maintenance of U(VI)-reducing conditions in the aquifer.
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Affiliation(s)
- Ping Zhang
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Zhili He
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Yujia Qin
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Ye Deng
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
- Research Center for Eco-Environmental Science, Chinese Academy of Sciences , Beijing 100085, China
| | - Liyou Wu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Qichao Tu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
- Department of Marine Sciences, Ocean College, Zhejiang University , Zhejiang, China
| | - Jianjun Wang
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences , Nanjing 210008, China
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University , Bozeman, Montana 59717, United States
| | - Terry C Hazen
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Adam P Arkin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington , Seattle, Washington 98105, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University , Beijing 100084, China
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Sánchez O. Constructed Wetlands Revisited: Microbial Diversity in the -omics Era. MICROBIAL ECOLOGY 2017; 73:722-733. [PMID: 27832305 DOI: 10.1007/s00248-016-0881-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/17/2016] [Indexed: 06/06/2023]
Abstract
Constructed wetlands (CWs) constitute an interesting alternative option to conventional systems for wastewater treatment. This technology is based on the utilization of the concerted activity of microorganisms for the removal of contaminants. Consequently, knowledge on the microbial assemblages dwelling CWs and the different environmental factors which can alter their activities is crucial for understanding their performance. In the last decades, the use of molecular techniques to characterize these communities and more recently, application of -omics tools, have broaden our view of microbial diversity and function in wastewater microbiology. In this manuscript, a review of the current knowledge on microbial diversity in CWs is offered, placing particular emphasis on the different molecular studies carried out in this field. The effect of environmental conditions, such as plant species, hydraulic design, water depth, organic carbon, temperature and substrate type on prokaryotic communities has been carefully revised, and the different studies highlight the importance of these factors in carbon, nitrogen and sulfur cycles. Overall, the novel -omics open a new horizon to study the diversity and ecophysiology of microbial assemblages and their interactions in CWs, particularly for those microorganisms belonging to the rare biosphere not detectable with conventional molecular techniques.
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Affiliation(s)
- Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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47
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Jones AA, Bennett PC. Mineral Ecology: Surface Specific Colonization and Geochemical Drivers of Biofilm Accumulation, Composition, and Phylogeny. Front Microbiol 2017; 8:491. [PMID: 28400754 PMCID: PMC5368280 DOI: 10.3389/fmicb.2017.00491] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 03/09/2017] [Indexed: 01/30/2023] Open
Abstract
This study tests the hypothesis that surface composition influences microbial community structure and growth of biofilms. We used laboratory biofilm reactors (inoculated with a diverse subsurface community) to explore the phylogenetic and taxonomic variability in microbial communities as a function of surface type (carbonate, silicate, aluminosilicate), media pH, and carbon and phosphate availability. Using high-throughput pyrosequencing, we found that surface type significantly controlled ~70–90% of the variance in phylogenetic diversity regardless of environmental pressures. Consistent patterns also emerged in the taxonomy of specific guilds (sulfur-oxidizers/reducers, Gram-positives, acidophiles) due to variations in media chemistry. Media phosphate availability was a key property associated with variation in phylogeny and taxonomy of whole reactors and was negatively correlated with biofilm accumulation and α-diversity (species richness and evenness). However, mineral-bound phosphate limitations were correlated with less biofilm. Carbon added to the media was correlated with a significant increase in biofilm accumulation and overall α-diversity. Additionally, planktonic communities were phylogenetically distant from those in biofilms. All treatments harbored structurally (taxonomically and phylogenetically) distinct microbial communities. Selective advantages within each treatment encouraged growth and revealed the presence of hundreds of additional operational taxonomix units (OTU), representing distinct consortiums of microorganisms. Ultimately, these results provide evidence that mineral/rock composition significantly influences microbial community structure, diversity, membership, phylogenetic variability, and biofilm growth in subsurface communities.
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Affiliation(s)
- Aaron A Jones
- Department of Geological Sciences, University of Texas at Austin Austin, TX, USA
| | - Philip C Bennett
- Department of Geological Sciences, University of Texas at Austin Austin, TX, USA
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48
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Pallares IG, Moore TC, Escalante-Semerena JC, Brunold TC. Spectroscopic Studies of the EutT Adenosyltransferase from Salmonella enterica: Evidence of a Tetrahedrally Coordinated Divalent Transition Metal Cofactor with Cysteine Ligation. Biochemistry 2017; 56:364-375. [PMID: 28045498 DOI: 10.1021/acs.biochem.6b00750] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The EutT enzyme from Salmonella enterica, a member of the family of ATP:cobalt(I) corrinoid adenosyltransferase (ACAT) enzymes, requires a divalent transition metal ion for catalysis, with Fe(II) yielding the highest activity. EutT contains a unique cysteine-rich HX11CCX2C(83) motif (where H and the last C occupy the 67th and 83rd positions, respectively, in the amino acid sequence) not found in other ACATs and employs an unprecedented mechanism for the formation of adenosylcobalamin. Recent kinetic and spectroscopic studies of this enzyme revealed that residues in the HX11CCX2C(83) motif are required for the tight binding of the divalent metal ion and are critical for the formation of a four-coordinate (4c) cob(II)alamin [Co(II)Cbl] intermediate in the catalytic cycle. However, it remained unknown which, if any, of the residues in the HX11CCX2C(83) motif bind the divalent metal ion. To address this issue, we have characterized Co(II)-substituted wild-type EutT (EutTWT/Co) by using electronic absorption, electron paramagnetic resonance, and magnetic circular dichroism (MCD) spectroscopies. Our results indicate that the reduced catalytic activity of EutTWT/Co relative to that of the Fe(II)-containing enzyme arises from the incomplete incorporation of Co(II) ions and, thus, a decrease in the relative population of 4c Co(II)Cbl. Our MCD data for EutTWT/Co also reveal that the Co(II) ions reside in a distorted tetrahedral coordination environment with direct cysteine sulfur ligation. Additional spectroscopic studies of EutT/Co variants possessing a single alanine substitution of either His67, His75, Cys79, Cys80, or Cys83 indicate that Cys80 coordinates to the Co(II) ion, while the additional residues are important for maintaining the structural integrity and/or high affinity of the metal binding site.
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Affiliation(s)
- Ivan G Pallares
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Theodore C Moore
- Department of Microbiology, University of Georgia , Athens, Georgia 30602, United States
| | | | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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49
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Zhang S, Merino N, Wang N, Ruan T, Lu X. Impact of 6:2 fluorotelomer alcohol aerobic biotransformation on a sediment microbial community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 575:1361-1368. [PMID: 27756549 DOI: 10.1016/j.scitotenv.2016.09.214] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 06/06/2023]
Abstract
Sediment microbial communities are responsible for many chemical biotransformation processes in the aquatic environment and play a critical role in various ecosystems and biogeochemical cycling. However, the impact of polyfluoroalkyl substances on sediment microbial communities remains unclear. These substances are increasingly being used in consumer and industrial products to replace environmentally persistent perfluoroalkyl substances. In this study, we investigated the effects of low (5mg/L) and high (15mg/L) doses of 6:2 fluorotelomer alcohol [6:2 FTOH, F(CF2)6CH2CH2OH] on the structure of a sediment microbial community. 6:2 FTOH biotransformation was rapid in the sediment mixture with a half-life <3days, regardless of the initial doses. After 28days, major products produced in the high dose condition included 28mol% 5:2 sFTOH [F(CF2)5CH(OH)CH3], 9.6mol% 5:3 Acid [F(CF2)5CH2CH2COOH] and 11mol% PFHxA [F(CF2)5COOH], while 73mol% 5:2 sFTOH, 23mol% 5:3 Acid and 26mol% PFHxA were observed in the low dose condition. In the original (control) sediment without 6:2 FTOH dosing, Proteobacteria was the predominant microorganism (18%), followed by Chloroflexi (14%), Verrucomicrobia (13%), Firmicutes (3.4%), Bacterioidetes (2.4%), Actinobacteria (1.7%) and Planctomycetes (1.3%). The presence of 6:2 FTOH and the accumulation of transient transformation products in the sediment exerted selection pressure on the microbial taxonomic distribution and diversity. Our observations indicate that potential 6:2 FTOH degraders and tolerant strains, such as Dokdonella spp., Thauera spp., Albidovulum spp. and Caldanaerovirga spp., existed in the sediment mixture and began to dominate over time. This suggests that these genera might have higher tolerance towards elevated 6:2 FTOH and its transformation products. These findings on the characterization of sediment microbial community stability and dynamics will help predict changes in response to perfluoroalkyl and polyfluoroalkyl substances and also help identify robust microbial strains to degrade polyfluoroalkyl substances in the environment.
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Affiliation(s)
- Shu Zhang
- Laboratory for Earth Surface Processes, Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Nancy Merino
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Ning Wang
- 132 Shrewsbury Dr., Wilmington, DE 19810, USA.
| | - Ting Ruan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Xiaoxia Lu
- Laboratory for Earth Surface Processes, Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
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50
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Colin Y, Goñi-Urriza M, Gassie C, Carlier E, Monperrus M, Guyoneaud R. Distribution of Sulfate-Reducing Communities from Estuarine to Marine Bay Waters. MICROBIAL ECOLOGY 2017; 73:39-49. [PMID: 27581035 DOI: 10.1007/s00248-016-0842-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/17/2016] [Indexed: 06/06/2023]
Abstract
Estuaries are highly dynamic ecosystems in which freshwater and seawater mix together. Depending on tide and river inflows, particles originating from rivers or from the remobilization of sediments accumulate in the water column. Due to the salinity gradient and the high heterotrophic activity in the estuarine plume, hypoxic and anoxic microniches may form in oxygenated waters, sustaining favorable conditions for resuspended anaerobic microorganisms. In this context, we tested the hypothesis that anaerobic sulfate-reducing prokaryotes may occur in the water column of the Adour River. Using 16S ribosomal RNA (rRNA) and dsrAB-based terminal restriction fragment length polymorphism (T-RFLP) techniques, we characterized total prokaryotic and sulfate-reducing communities along a gradient from estuarine to marine bay waters. Sulfate-reducing prokaryotes were further characterized by the description of dsrB genes and the cultivation of sulfidogenic anaerobic microorganisms. As a result, physical-chemical parameters had a significant effect on water bacterial diversity and community structure along the studied gradient. The concentration of cultured sulfidogenic microorganisms ranged from 1 to 60 × 103 cells l-1 in the water column. Sulfate-reducing prokaryotes occurring in estuarine waters were closely related to microorganisms previously detected in freshwater sediments, suggesting an estuarine origin, mainly by the remobilization of the sediments. In the marine bay station, sediment-derived sulfate-reducing prokaryotes were not cultured anymore, probably due to freshwater dilution, increasing salinity and extended oxic stress. Nevertheless, isolates related to the type strain Desulfovibrio oceani were cultured from the diluted plume and deep marine waters, indicating the occurrence of autochthonous sulfate-reducing bacteria offshore.
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Affiliation(s)
- Yannick Colin
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France.
- INRA, UMR 1136 INRA/Université de Lorraine, Interactions Arbres Micro-organismes, Centre de Nancy, 54280, Champenoux, France.
| | - Marisol Goñi-Urriza
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France
| | - Claire Gassie
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France
| | - Elisabeth Carlier
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France
| | - Mathilde Monperrus
- Laboratoire de Chimie Analytique Bio-Inorganique et Environnement (LCABIE), IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, Pau, France
| | - Rémy Guyoneaud
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France
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