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Hiralal A, Geelhoed JS, Neukirchen S, Meysman FJR. Comparative genomic analysis of nickel homeostasis in cable bacteria. BMC Genomics 2024; 25:692. [PMID: 39009997 PMCID: PMC11247825 DOI: 10.1186/s12864-024-10594-7] [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: 03/27/2024] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
BACKGROUND Cable bacteria are filamentous members of the Desulfobulbaceae family that are capable of performing centimetre‑scale electron transport in marine and freshwater sediments. This long‑distance electron transport is mediated by a network of parallel conductive fibres embedded in the cell envelope. This fibre network efficiently transports electrical currents along the entire length of the centimetre‑long filament. Recent analyses show that these fibres consist of metalloproteins that harbour a novel nickel‑containing cofactor, which indicates that cable bacteria have evolved a unique form of biological electron transport. This nickel‑dependent conduction mechanism suggests that cable bacteria are strongly dependent on nickel as a biosynthetic resource. Here, we performed a comprehensive comparative genomic analysis of the genes linked to nickel homeostasis. We compared the genome‑encoded adaptation to nickel of cable bacteria to related members of the Desulfobulbaceae family and other members of the Desulfobulbales order. RESULTS Presently, four closed genomes are available for the monophyletic cable bacteria clade that consists of the genera Candidatus Electrothrix and Candidatus Electronema. To increase the phylogenomic coverage, we additionally generated two closed genomes of cable bacteria: Candidatus Electrothrix gigas strain HY10‑6 and Candidatus Electrothrix antwerpensis strain GW3‑4, which are the first closed genomes of their respective species. Nickel homeostasis genes were identified in a database of 38 cable bacteria genomes (including 6 closed genomes). Gene prevalence was compared to 19 genomes of related strains, residing within the Desulfobulbales order but outside of the cable bacteria clade, revealing several genome‑encoded adaptations to nickel homeostasis in cable bacteria. Phylogenetic analysis indicates that nickel importers, nickel‑binding enzymes and nickel chaperones of cable bacteria are affiliated to organisms outside the Desulfobulbaceae family, with several proteins showing affiliation to organisms outside of the Desulfobacterota phylum. Conspicuously, cable bacteria encode a unique periplasmic nickel export protein RcnA, which possesses a putative cytoplasmic histidine‑rich loop that has been largely expanded compared to RcnA homologs in other organisms. CONCLUSION Cable bacteria genomes show a clear genetic adaptation for nickel utilization when compared to closely related genera. This fully aligns with the nickel‑dependent conduction mechanism that is uniquely found in cable bacteria.
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Affiliation(s)
- Anwar Hiralal
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
| | | | - Sinje Neukirchen
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
| | - Filip J R Meysman
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium.
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
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Shang Y, Wang X, Wu X, Dou H, Wei Q, Wang Q, Liu G, Sun G, Wang L, Zhang H. Bacterial and fungal community structures in Hulun Lake are regulated by both stochastic processes and environmental factors. Microbiol Spectr 2024; 12:e0324523. [PMID: 38602397 PMCID: PMC11064641 DOI: 10.1128/spectrum.03245-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/13/2024] [Indexed: 04/12/2024] Open
Abstract
Microorganisms are a crucial component of lake ecosystems and significant contributors to biogeochemical cycles. However, the understanding of how primary microorganism groups (e.g., bacteria and fungi) are distributed and constructed within different lake habitats is lacking. We investigated the bacterial and fungal communities of Hulun Lake using high-throughput sequencing techniques targeting 16S rRNA and Internal Transcribed Spacer 2 genes, including a range of ecological and statistical methodologies. Our findings reveal that environmental factors have high spatial and temporal variability. The composition and community structures vary significantly depending on differences in habitats. Variance partitioning analysis showed that environmental and geographical factors accounted for <20% of the community variation. Canonical correlation analysis showed that among the environmental factors, temperature, pH, and dissolved oxygen had strong control over microbial communities. However, the microbial communities (bacterial and fungal) were primarily controlled by the dispersal limitations of stochastic processes. This study offers fresh perspectives regarding the maintenance mechanism of bacterial and fungal biodiversity in lake ecosystems, especially regarding the responses of microbial communities under identical environmental stress.IMPORTANCELake ecosystems are an important part of the freshwater ecosystem. Lake microorganisms play an important role in material circulation and energy flow owing to their unique enzymatic and metabolic capacity. In this study, we observed that bacterial and fungal communities varied widely in the water and sediments of Hulun Lake. The primary factor affecting their formation was identified as dispersal limitation during stochastic processes. Environmental and geographical factors accounted for <20% of the variation in bacterial and fungal communities, with pH, temperature, and dissolved oxygen being important environmental factors. Our findings provide new insights into the responses of bacteria and fungi to the environment, shed light on the ecological processes of community building, and deepen our understanding of lake ecosystems. The results of this study provide a reference for lake management and conservation, particularly with respect to monitoring and understanding microbial communities in response to environmental changes.
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Affiliation(s)
- Yongquan Shang
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Xibao Wang
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Xiaoyang Wu
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, China
| | - Qinguo Wei
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Qi Wang
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, China
| | - Gang Liu
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Guolei Sun
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Lidong Wang
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Honghai Zhang
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
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Chen X, Liu J, Zhu XY, Xue CX, Yao P, Fu L, Yang Z, Sun K, Yu M, Wang X, Zhang XH. Phylogenetically and metabolically diverse autotrophs in the world's deepest blue hole. ISME COMMUNICATIONS 2023; 3:117. [PMID: 37964026 PMCID: PMC10645885 DOI: 10.1038/s43705-023-00327-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023]
Abstract
The world's deepest yongle blue hole (YBH) is characterized by sharp dissolved oxygen (DO) gradients, and considerably low-organic-carbon and high-inorganic-carbon concentrations that may support active autotrophic communities. To understand metabolic strategies of autotrophic communities for obtaining carbon and energy spanning redox gradients, we presented finer characterizations of microbial community, metagenome and metagenome-assembled genomes (MAGs) in the YBH possessing oxic, hypoxic, essentially anoxic and completely anoxic zones vertically. Firstly, the YBH microbial composition and function shifted across the four zones, linking to different biogeochemical processes. The recovery of high-quality MAGs belonging to various uncultivated lineages reflected high novelty of the YBH microbiome. Secondly, carbon fixation processes and associated energy metabolisms varied with the vertical zones. The Calvin-Benson-Bassham (CBB) cycle was ubiquitous but differed in affiliated taxa at different zones. Various carbon fixation pathways were found in the hypoxic and essentially anoxic zones, including the 3-hyroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle affiliated to Nitrososphaeria, and Wood-Ljungdahl (WL) pathway affiliated to Planctomycetes, with sulfur oxidation and dissimilatory nitrate reduction as primary energy-conserving pathways. The completely anoxic zone harbored diverse taxa (Dehalococcoidales, Desulfobacterales and Desulfatiglandales) utilizing the WL pathway coupled with versatile energy-conserving pathways via sulfate reduction, fermentation, CO oxidation and hydrogen metabolism. Finally, most of the WL-pathway containing taxa displayed a mixotrophic lifestyle corresponding to flexible carbon acquisition strategies. Our result showed a vertical transition of microbial lifestyle from photo-autotrophy, chemoautotrophy to mixotrophy in the YBH, enabling a better understanding of carbon fixation processes and associated biogeochemical impacts with different oxygen availability.
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Affiliation(s)
- Xing Chen
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jiwen Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xiao-Yu Zhu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Chun-Xu Xue
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Liang Fu
- Sansha Track Ocean Coral Reef Conservation Research Institute, Sansha, 573199, China
| | - Zuosheng Yang
- College of Marine Geosciences, Ocean University of China, Qingdao, 266100, China
| | - Kai Sun
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Min Yu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xiaolei Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China.
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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Li Y, Xiong L, Zeng K, Wei Y, Li H, Ji X. Microbial-driven carbon fixation in natural wetland. J Basic Microbiol 2023; 63:1115-1127. [PMID: 37440152 DOI: 10.1002/jobm.202300273] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/15/2023] [Accepted: 07/01/2023] [Indexed: 07/14/2023]
Abstract
With the development of global industrialization, carbon neutrality has become an issue that we must be paid attention to. Microorganisms not only have an important impact on the carbon chemical cycle between the Earth's biosphere and biogeography but also play a key role in maintaining the global organic carbon balance. Wetlands are the main reservoir of organic carbon in the mainland of China, and wetland carbon sinks are indispensable for China to achieve the goal of "dual carbon," and China has taken the consolidation and improvement of wetland carbon sink capacity as an important part of the carbon peaking action plan. As a unique low-latitude, high-altitude seasonal plateau wetland in China, Napahai shows high research value. However, the role of microbes in maintaining dissolved organic carbon balance in this area has not been reported. In the study, six carbon fixation genes, accA, aclB, acsA, acsB, cbbL, and rbcL, were analyzed based on metagenomics to elucidate the rich genetic diversity, uniqueness and differences in the Napahai plateau wetland. It was found that the microbial diversity in the Napahai plateau wetland was different from other habitats. In addition, the aclB gene, a rare taxon with high genetic diversity and rich species in the Napahai plateau wetland, played a key role in the microbial metabolic pathway. Finally, the construction of a metabolic pathway through the Kyoto encyclopedia for genes and genomes revealed the contribution of microbes to carbon fixation and the role of microbes in maintaining the organic carbon balance of the Napahai plateau wetland.
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Affiliation(s)
- Yanmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Lingling Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Kun Zeng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, China
| | - Xiuling Ji
- Medical School, Kunming University of Science and Technology, Kunming, China
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Lomakina A, Bukin S, Shubenkova O, Pogodaeva T, Ivanov V, Bukin Y, Zemskaya T. Microbial Communities in Ferromanganese Sediments from the Northern Basin of Lake Baikal (Russia). Microorganisms 2023; 11:1865. [PMID: 37513037 PMCID: PMC10386581 DOI: 10.3390/microorganisms11071865] [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: 06/29/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
We analyzed the amplicons of the 16S rRNA genes and assembled metagenome-assembled genomes (MAGs) of the enrichment culture from the Fe-Mn layer to have an insight into the diversity and metabolic potential of microbial communities from sediments of two sites in the northern basin of Lake Baikal. Organotrophic Chloroflexota, Actionobacteriota, and Acidobacteriota, as well as aerobic and anaerobic participants of the methane cycle (Methylococcales and Methylomirabilota, respectively), dominated the communities of the surface layers. With depth, one of the cores showed a decrease in the proportion of the Chloroflexota and Acidobacteriota members and a substantial increase in the sequences of the phylum Firmicutes. The proportion of the Desulfobacteriota and Thermodesulfovibronia (Nitrospirota) increased in another core. The composition of archaeal communities was similar between the investigated sites and differed in depth. Members of ammonia-oxidizing archaea (Nitrososphaeria) predominated in the surface sediments, with an increase in anaerobic methanotrophs (Methanoperedenaceae) and organoheterotrophs (Bathyarchaeia) in deep sediments. Among the 37 MAGs, Gammaproteobacteria, Desulfobacteriota, and Methylomirabilota were the most common in the microbial community. Metagenome sequencing revealed the assembled genomes genes for N, S, and CH4 metabolism for carbon fixation, and genes encoding Fe and Mn pathways, indicating the likely coexistence of the biogeochemical cycle of various elements and creating certain conditions for the development of taxonomically and functionally diverse microbial communities.
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Affiliation(s)
- Anna Lomakina
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences (LIN SB RAS), 664033 Irkutsk, Russia
| | - Sergei Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences (LIN SB RAS), 664033 Irkutsk, Russia
| | - Olga Shubenkova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences (LIN SB RAS), 664033 Irkutsk, Russia
| | - Tatyana Pogodaeva
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences (LIN SB RAS), 664033 Irkutsk, Russia
| | - Vyacheslav Ivanov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences (LIN SB RAS), 664033 Irkutsk, Russia
| | - Yuri Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences (LIN SB RAS), 664033 Irkutsk, Russia
| | - Tamara Zemskaya
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences (LIN SB RAS), 664033 Irkutsk, Russia
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6
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Huang J, Yang J, Han M, Wang B, Sun X, Jiang H. Microbial carbon fixation and its influencing factors in saline lake water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162922. [PMID: 36933719 DOI: 10.1016/j.scitotenv.2023.162922] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 05/06/2023]
Abstract
Microbial carbon fixation in saline lakes constitutes an important part of the global lacustrine carbon budget. However, the microbial inorganic carbon uptake rates in saline lake water and its influencing factors are still not fully understood. Here, we studied in situ microbial carbon uptake rates under light-dependent and dark conditions in the saline water of Qinghai Lake using a carbon isotopic labeling (14C-bicarbonate) technique, followed by geochemical and microbial analyses. The results showed that the light-dependent inorganic carbon uptake rates were 135.17-293.02 μg C L-1 h-1 during the summer cruise, while dark inorganic carbon uptake rates ranged from 4.27 to 14.10 μg C L-1 h-1. Photoautotrophic prokaryotes and algae (e.g. Oxyphotobacteria, Chlorophyta, Cryptophyta and Ochrophyta) may be the major contributors to light-dependent carbon fixation processes. Microbial inorganic carbon uptake rates were mainly influenced by the level of nutrients (e.g., ammonium, dissolved inorganic carbon, dissolved organic carbon, total nitrogen), with dissolved inorganic carbon content being predominant. Environmental and microbial factors jointly regulate the total, light-dependent and dark inorganic carbon uptake rates in the studied saline lake water. In summary, microbial light-dependent and dark carbon fixation processes are active and contribute significantly to carbon sequestration in saline lake water. Therefore, more attention should be given to microbial carbon fixation and its response to climate and environmental changes of the lake carbon cycle in the context of climate change.
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Affiliation(s)
- Jianrong Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Mingxian Han
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Xiaoxi Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China.
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Tan C, Zhang W, Wei Y, Zhao N, Li J. Insights into nitrogen removal and microbial response of marine anammox bacteria-based consortia treating saline wastewater: From high to moderate and low salinities. BIORESOURCE TECHNOLOGY 2023; 382:129220. [PMID: 37217147 DOI: 10.1016/j.biortech.2023.129220] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 05/24/2023]
Abstract
Marine anammox bacteria (MAB) have promising nitrogen removal performance in high saline wastewater treatment. Nevertheless, the impact resulting from moderate and low salinities on MAB is still unclear. Herein, MAB were applied to treat saline wastewater from high to moderate and low salinities for the first time. Independent of salinities (35-3.5 g/L), MAB consistently exhibited good nitrogen removal performance, and maximum total nitrogen removal rate (0.97 kg/(m3·d)) occurred at 10.5 g/L salts. More extracellular polymeric substances (EPSs) were secreted by MAB-based consortia to resist hypotonic surroundings. However, a sharp EPS decrease was accompanied by the collapse of MAB-driven anammox process, and MAB granules disintegrated due to long-term exposure to salt-free environment. The relative abundance of MAB varied from 10.7% to 15.9% and 3.8% as salinity decreased from 35 to 10.5 and 0 g/L salts. These findings will provide practical implementation of MAB-driven anammox process treating wastewater with different salinities.
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Affiliation(s)
- Chen Tan
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Weidong Zhang
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Yunna Wei
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Na Zhao
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Jin Li
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China.
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Sereika M, Petriglieri F, Jensen TBN, Sannikov A, Hoppe M, Nielsen PH, Marshall IPG, Schramm A, Albertsen M. Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria. THE ISME JOURNAL 2023; 17:561-569. [PMID: 36697964 PMCID: PMC10030654 DOI: 10.1038/s41396-023-01372-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
Cable bacteria of the Desulfobulbaceae family are centimeter-long filamentous bacteria, which are capable of conducting long-distance electron transfer. Currently, all cable bacteria are classified into two candidate genera: Candidatus Electronema, typically found in freshwater environments, and Candidatus Electrothrix, typically found in saltwater environments. This taxonomic framework is based on both 16S rRNA gene sequences and metagenome-assembled genome (MAG) phylogenies. However, most of the currently available MAGs are highly fragmented, incomplete, and thus likely miss key genes essential for deciphering the physiology of cable bacteria. Also, a closed, circular genome of cable bacteria has not been published yet. To address this, we performed Nanopore long-read and Illumina short-read shotgun sequencing of selected environmental samples and a single-strain enrichment of Ca. Electronema aureum. We recovered multiple cable bacteria MAGs, including two circular and one single-contig. Phylogenomic analysis, also confirmed by 16S rRNA gene-based phylogeny, classified one circular MAG and the single-contig MAG as novel species of cable bacteria, which we propose to name Ca. Electronema halotolerans and Ca. Electrothrix laxa, respectively. The Ca. Electronema halotolerans, despite belonging to the previously recognized freshwater genus of cable bacteria, was retrieved from brackish-water sediment. Metabolic predictions showed several adaptations to a high salinity environment, similar to the "saltwater" Ca. Electrothrix species, indicating how Ca. Electronema halotolerans may be the evolutionary link between marine and freshwater cable bacteria lineages.
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Affiliation(s)
- Mantas Sereika
- Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | | | | | - Artur Sannikov
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Morten Hoppe
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | | | - Ian P G Marshall
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
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Guan X, He R, Zhang B, Gao C, Liu F. Seasonal variations of microbial community structure, assembly processes, and influencing factors in karst river. Front Microbiol 2023; 14:1133938. [PMID: 37032860 PMCID: PMC10075313 DOI: 10.3389/fmicb.2023.1133938] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/03/2023] [Indexed: 04/11/2023] Open
Abstract
The physicochemical properties and microbial communities have significant annual and seasonal changes in karst aquifers. To explore the changes of microbial community and their relationships with environmental factors, water samples were collected from a typical karst river. Microbial communities in winter (Jan-2017 and Jan-2019) were stable with high similarity in spite of the 2 years sampling interval, but the microbial communities in Aug-2017 was different from that in Aug-2018. In four sampling times, there were 275 shared genera, whose average relative abundance ranging from 89.04 to 96.27%. The winter and summer specific genera were mainly from the recharge of tributary site K6 and discharge of waste water treatment plant (K2 and K3), respectively. The deterministic processes had a more significant effect on the microbial community assembly in winter than that in summer, which was affected by environmental pressure from pollution. Furthermore, antibiotics and inorganic nitrogen pollution affected element cycles of nitrogen and sulfur indirectly through microbial ecological modules in karst river, and the denitrification and desulfurization processes were potentially inhibited. These findings contributed to understand the changes and its assembly mechanism of microbial community, as well as the feedback to environment in polluted karst river.
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Affiliation(s)
- Xiangyu Guan
- School of Ocean Sciences, China University of Geosciences, Beijing, China
| | - Ruoxue He
- School of Ocean Sciences, China University of Geosciences, Beijing, China
- Department of Discipline Construction and Technology Development, Chengdu Technological University, Chengdu, China
| | - Biao Zhang
- School of Ocean Sciences, China University of Geosciences, Beijing, China
| | - Chengjie Gao
- Beijing Municipal Research Institute of Eco-Environmental Protection, Beijing, China
| | - Fei Liu
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing, China
- *Correspondence: Fei Liu,
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