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Sorokin DY, Merkel AY, Kolganova TV, Bale NJ, Sinninghe Damsté JS. Natronospira bacteriovora sp. nov., and Natronospira elongata sp. nov., extremely salt-tolerant predatory proteolytic bacteria from soda lakes and proposal to classify the genus Natronospira into Natronospiraceae fam. nov., and Natronospirales ord. nov., within the class Gammaproteobacteria. Syst Appl Microbiol 2024; 47:126519. [PMID: 38759530 DOI: 10.1016/j.syapm.2024.126519] [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: 03/20/2024] [Revised: 05/14/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
The genus Natronospira is represented by a single species of extremely salt-tolerant aerobic alkaliphilic proteolytic bacterium, isolated from hypersaline soda lakes. When cells of Gram-positive cocci were used as a substrate instead of proteins at extremely haloalkaline conditions, two new members of this genus were enriched and isolated in pure culture from the same sites. Strains AB-CW1 and AB-CW4 are obligate aerobic heterotrophic proteolytic bacteria able to feed on both live and dead cells of staphylococci and a range of proteins and peptides. Similar to the type species, N. proteinivora, the isolates are extremely salt-tolerant obligate alkaliphiles. However, N. proteinivora was unable to use bacterial cells as a substrate. Electron microscopy showed direct contact between the prey and predator cells. Functional analysis of the AB-CW1 and AB-CW4 genomes identified two sets of genes coding for extracellular enzymes potentially involved in the predation and proteolysis, respectively. The first set includes several copies of lysozyme-like GH23 peptidoglycan-lyase and murein-specific M23 [Zn]-di-peptidase enabling the cell wall degradation. The second set features multiple copies of secreted serine and metallopeptidases apparently allowing for the strong proteolytic phenotype. Phylogenomic analysis placed the isolates into the genus Natronospira as two novel species members, and furthermore indicated that this genus forms a deep-branching lineage of a new family (Natronospiraceae) and order (Natronospirales) within the class Gammaproteobacteria. On the basis of distinct phenotypic and genomic properties, strain AB-CW1T (JCM 335396 = UQM 41579) is proposed to be classified as Natronospira elongata sp. nov., and AB-CW4T (JCM 335397 = UQM 41580) as Natronospira bacteriovora sp. nov.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia; Department of Biotechnology, TU Delft, The Netherlands.
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Tatyana V Kolganova
- Skryabin Insitutute of Bioengineering, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg, Texel, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg, Texel, The Netherlands
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Khomyakova MA, Merkel AY, Slobodkin AI. Anaerobaca lacustris gen. nov., sp. nov., an obligately anaerobic planctomycete of the widespread SG8-4 group, isolated from a coastal lake, and proposal of Anaerobacaceae fam. nov. Syst Appl Microbiol 2024; 47:126522. [PMID: 38852331 DOI: 10.1016/j.syapm.2024.126522] [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: 04/22/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
One of the numerous and widespread lineages of planctomycetes is the hitherto uncultured SG8-4 group inhabiting anoxic environments. A novel anaerobic, mesophilic, alkalitolerant, chemoorganotrophic bacterium (strain M17dextrT) was isolated from anaerobic sediment of a coastal lake (Taman Peninsula, Russia). The cell were mainly non-motile cocci, 0.3 to 1.0 µm in diameter forming chains or aggregates. The cells had a Gram-negative cell wall and divided by binary fission. The temperature range for growth was 20-37 0C (optimum at 30 0C). The pH range for growth was 6.5-10.0, with an optimum at pH 8.0-8.5. Strain M17dextrT fermented mono-, di- and polysaccharides (starch, xanthan gum, dextran, N-acetylglucosamine), but did not utilized proteinaceous compounds. Major cellular fatty acids were C16:0 and C18:0. The genome of strain M17dextrT had a size of 5.7 Mb with a G + C content of 62.49 %. The genome contained 345 CAZyme genes. The closest cultured phylogenetic relatives of strain M17dextrT were members of the order Sedimentisphaerales, class Phycisphaerae. Among characterized planctomycetes, the highest 16S rRNA gene sequence similarity (88.3 %) was observed with Anaerohalosphaera lusitana. According to phylogenomic analysis strain M17dextrT together with many uncultured representatives of Sedimentisphaerales forms a separate family-level lineage. We propose to assign strain M17dextrT to a novel genus and species, Anaerobaca lacustris gen. nov., sp. nov.; the type strain is M17dextrT (=VKM B-3571 T = DSM 113417 T = JCM 39238 T = KCTC 25381 T = UQM 41474 T). This genus is placed in a novel family, Anaerobacaceae fam. nov. within the order Sedimentisphaerales.
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Affiliation(s)
- M A Khomyakova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia.
| | - A Y Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | - A I Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
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Stewart DI, Vasconcelos EJR, Burke IT, Baker A. Metagenomes from microbial populations beneath a chromium waste tip give insight into the mechanism of Cr (VI) reduction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172507. [PMID: 38657818 DOI: 10.1016/j.scitotenv.2024.172507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 04/04/2024] [Accepted: 04/13/2024] [Indexed: 04/26/2024]
Abstract
Dumped Chromium Ore Processing Residue (COPR) at legacy sites poses a threat to health through leaching of toxic Cr(VI) into groundwater. Previous work implicates microbial activity in reducing Cr(VI) to less mobile and toxic Cr(III), but the mechanism has not been explored. To address this question a combined metagenomic and geochemical study was undertaken. Soil samples from below the COPR waste were used to establish anaerobic microcosms which were challenged with Cr(VI), with or without acetate as an electron donor, and incubated for 70 days. Cr was rapidly reduced in both systems, which also reduced nitrate, nitrite then sulfate, but this sequence was accelerated in the acetate amended microcosms. 16S rRNA gene sequencing revealed that the original soil sample was diverse but both microcosm systems became less diverse by the end of the experiment. A high proportion of 16S rRNA gene reads and metagenome-assembled genomes (MAGs) with high completeness could not be taxonomically classified, highlighting the distinctiveness of these alkaline Cr impacted systems. Examination of the coding capacity revealed widespread capability for metal tolerance and Fe uptake and storage, and both populations possessed metabolic capability to degrade a wide range of organic molecules. The relative abundance of genes for fatty acid degradation was 4× higher in the unamended compared to the acetate amended system, whereas the capacity for dissimilatory sulfate metabolism was 3× higher in the acetate amended system. We demonstrate that naturally occurring in situ bacterial populations have the metabolic capability to couple acetate oxidation to sequential reduction of electron acceptors which can reduce Cr(VI) to less mobile and toxic Cr(III), and that microbially produced sulfide may be important in reductive precipitation of chromate. This capability could be harnessed to create a Cr(VI) trap-zone beneath COPR tips without the need to disturb the waste.
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Affiliation(s)
- Douglas I Stewart
- School of Civil Engineering, University of Leeds, Leeds LS2 9JT, UK.
| | | | - Ian T Burke
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK.
| | - Alison Baker
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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Lawruk-Desjardins C, Storck V, Ponton DE, Amyot M, Walsh DA. A genome catalogue of mercury-methylating bacteria and archaea from sediments of a boreal river facing human disturbances. Environ Microbiol 2024; 26:e16669. [PMID: 38922750 DOI: 10.1111/1462-2920.16669] [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: 12/18/2023] [Accepted: 05/23/2024] [Indexed: 06/28/2024]
Abstract
Methyl mercury, a toxic compound, is produced by anaerobic microbes and magnifies in aquatic food webs, affecting the health of animals and humans. The exploration of mercury methylators based on genomes is still limited, especially in the context of river ecosystems. To address this knowledge gap, we developed a genome catalogue of potential mercury-methylating microorganisms. This was based on the presence of hgcAB from the sediments of a river affected by two run-of-river hydroelectric dams, logging activities and a wildfire. Through the use of genome-resolved metagenomics, we discovered a unique and diverse group of mercury methylators. These were dominated by members of the metabolically versatile Bacteroidota and were particularly rich in microbes that ferment butyrate. By comparing the diversity and abundance of mercury methylators between sites subjected to different disturbances, we found that ongoing disturbances, such as the input of organic matter related to logging activities, were particularly conducive to the establishment of a mercury-methylating niche. Finally, to gain a deeper understanding of the environmental factors that shape the diversity of mercury methylators, we compared the mercury-methylating genome catalogue with the broader microbial community. The results suggest that mercury methylators respond to environmental conditions in a manner similar to the overall microbial community. Therefore, it is crucial to interpret the diversity and abundance of mercury methylators within their specific ecological context.
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Affiliation(s)
| | - Veronika Storck
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Département de sciences biologiques, Université de Montréal, Montreal, Quebec, Canada
| | - Dominic E Ponton
- Département de sciences biologiques, Université de Montréal, Montreal, Quebec, Canada
| | - Marc Amyot
- Département de sciences biologiques, Université de Montréal, Montreal, Quebec, Canada
| | - David A Walsh
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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Geng L, Yang L, Liu T, Zhang S, Sun X, Wang W, Pan H, Yan L. Higher diversity of sulfur-oxidizing bacteria based on soxB gene sequencing in surface water than in spring in Wudalianchi volcanic group, NE China. Int Microbiol 2024:10.1007/s10123-024-00526-6. [PMID: 38740654 DOI: 10.1007/s10123-024-00526-6] [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: 12/30/2023] [Revised: 04/26/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024]
Abstract
INTRODUCTION Sulfur-oxidizing bacteria (SOB) play a key role in the biogeochemical cycling of sulfur. OBJECTIVES To explore SOB diversity, distribution, and physicochemical drivers in five volcanic lakes and two springs in the Wudalianchi volcanic field, China. METHODS This study analyzed microbial communities in samples via high-throughput sequencing of the soxB gene. Physical-chemical parameters were measured, and QIIME 2 (v2019.4), R, Vsearch, MEGA7, and Mothur processed the data. Alpha diversity indices and UPGMA clustering assessed community differences, while heat maps visualized intra-sample variations. Canoco 5.0 analyzed community-environment correlations, and NMDS, Adonis, and PcoA explored sample dissimilarities and environmental factor correlations. SPSS v.18.0 tested for statistical significance. RESULTS The diversity of SOB in surface water was higher than in springs (more than 7.27 times). We detected SOB affiliated to β-proteobacteria (72.3 %), α-proteobacteria (22.8 %), and γ-proteobacteria (4.2 %) distributed widely in these lakes and springs. Rhodoferax and Cupriavidus were most frequent in all water samples, while Rhodoferax and Bradyrhizobium are dominant in surface waters but rare in springs. SOB genera in both habitats were positively correlated. Co-occurrence analysis identified Bradyrhizobium, Blastochloris, Methylibium, and Metyhlobacterium as potential keystone taxa. Redundancy analysis (RDA) revealed positive correlations between SOB diversity and total carbon (TC), Fe2+, and total nitrogen (TN) in all water samples. CONCLUSION The diversity and community structure of SOB in volcanic lakes and springs in the Wudalianchi volcanic group were clarified. Moreover, the diversity and abundance of SOB decreased with the variation of water openness, from open lakes to semi-enclosed lakes and enclosed lakes.
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Affiliation(s)
- Lirong Geng
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Lei Yang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Tao Liu
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Shuang Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Xindi Sun
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
- Key Laboratory of Low‑carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs P. R. China, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Hong Pan
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Science, Harbin, 150090, Heilongjiang, China
| | - Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China.
- Key Laboratory of Low‑carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs P. R. China, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
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Sorokin DY, Elcheninov AG, Bale NJ, Sininghe Damsté J, Kublanov IV. Natronosalvus hydrolyticus sp. nov., a beta-1,3-glucan utilizing natronoarchaeon from hypersaline soda lakes. Syst Appl Microbiol 2024; 47:126514. [PMID: 38735274 DOI: 10.1016/j.syapm.2024.126514] [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: 03/05/2024] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024]
Abstract
Use of curldlan, an insoluble β-1,3-glucan, as an enrichment substrate under aerobic conditions resulted in the selection from hypersaline soda lakes of a single natronarchaeon, strain AArc-curdl1. This organism is an obligately aerobic saccharolytic, possessing a poorly explored (in Archaea) potential to utilize beta-1-3 glucans, being only a second example of a haloarchaeon with this ability known in pure culture. The main phenotypic property of the isolate is the ability to grow with insoluble β-1,3-backboned glucans, i.e. curdlan and pachyman. Furthermore, the strain utilized starch family α-glucans, beta-fructan inulin and a limited spectrum of sugars. The major ether-bound membrane polar phospholipids included PGP-Me and PG. The glyco- and sulfolipids were absent. The major respiratory menaquinone is MK-8:8. According to phylogenomic analysis, AArc-curdl1 represents a separate species in the recently described genus Natronosalvus within the family Natrialbaceae. The closest related species is Natronosalvus amylolyticus (ANI, AAI and DDH values of 90.2, 91.6 and 44 %, respectively). On the basis of its unique physiological properties and phylogenomic distance, strain AArc-curdl1T is classified as a novel species Natronosalvus hydrolyticus sp. nov. (=JCM 34865 = UQM 41566).
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia; Department of Biotechnology, Delft University of Technology, Delft, the Netherlands.
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nicole J Bale
- NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Texel, the Netherlands
| | - Jaap Sininghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Texel, the Netherlands
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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Aguilar C, Alwali A, Mair M, Rodriguez-Orduña L, Contreras-Peruyero H, Modi R, Roberts C, Sélem-Mojica N, Licona-Cassani C, Parkinson EI. Actinomycetota bioprospecting from ore-forming environments. Microb Genom 2024; 10:001253. [PMID: 38743050 PMCID: PMC11165632 DOI: 10.1099/mgen.0.001253] [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: 11/21/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
Natural products from Actinomycetota have served as inspiration for many clinically relevant therapeutics. Despite early triumphs in natural product discovery, the rate of unearthing new compounds has decreased, necessitating inventive approaches. One promising strategy is to explore environments where survival is challenging. These harsh environments are hypothesized to lead to bacteria developing chemical adaptations (e.g. natural products) to enable their survival. This investigation focuses on ore-forming environments, particularly fluoride mines, which typically have extreme pH, salinity and nutrient scarcity. Herein, we have utilized metagenomics, metabolomics and evolutionary genome mining to dissect the biodiversity and metabolism in these harsh environments. This work has unveiled the promising biosynthetic potential of these bacteria and has demonstrated their ability to produce bioactive secondary metabolites. This research constitutes a pioneering endeavour in bioprospection within fluoride mining regions, providing insights into uncharted microbial ecosystems and their previously unexplored natural products.
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Affiliation(s)
- César Aguilar
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Amir Alwali
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Madeline Mair
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | | | | | - Ramya Modi
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Carson Roberts
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | | | | | - Elizabeth Ivy Parkinson
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
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Gago JF, Viver T, Urdiain M, Ferreira E, Robledo P, Rossello-Mora R. Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode. Syst Appl Microbiol 2024; 47:126506. [PMID: 38640749 DOI: 10.1016/j.syapm.2024.126506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/21/2024]
Abstract
Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island of Balearic archipelago, harbours a variety of thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding the regional average). The metagenomes of two aquifers in the centre and southern of the island showed Pseudomonadota to be the most represented phylum when using extracted 16S rRNA gene sequences. However, the microbial structures within and between aquifers were remarkably diverse but similar in their metabolic profiles as revealed by the metagenome-assembled genomes (MAGs) pointing to a prevalence of aerobic chemolithoautotrophic and heterotrophic metabolisms, especially in the Llucmajor aquifer. Also, some evidences of anaerobic lifestyles were detected, which would indicate that these environments either could suffer episodes of oxygen depletion or the anaerobes had been transported from deeper waters. We believe that the local environmental factors (temperature, external inputs or chemistry) seem to be more relevant than the connection and, eventually, transport of microbial cells within the aquifer in determining the highly divergent structures. Notably, most of the reconstructed genomes belonged to undescribed bacterial lineages and from them two high-quality MAGs could be classified as novel taxa named following the rules of the Code for Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Accordingly, we propose the new species and genus Costitxia debesea gen. nov., sp. nov., affiliated with the novel family Costitxiaceae fam. nov., order Costitxiales ord. nov. and class Costitxiia class. nov.; and the new new species and genus Lloretia debesea gen. nov. sp. nov. affiliated with the novel family Lloretiaceae fam. nov.
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Affiliation(s)
- Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; The Deep Blue Sea Enterprise S.L., Barcelona, Spain; Lipotrue S.L., Barcelona, Spain.
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Elaine Ferreira
- The Deep Blue Sea Enterprise S.L., Barcelona, Spain; Lipotrue S.L., Barcelona, Spain
| | - Pedro Robledo
- Unit of Geological and Mining Institute of Spain in Balearic Islands (IGME-CSIC), Palma de Mallorca, Spain
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
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Huang Q, Yang F, Cao H, Cheng J, Jiang M, Li M, Ni H, Xie L. Comparison of Microbial Diversity of Two Typical Volcanic Soils in Wudalianchi, China. Microorganisms 2024; 12:656. [PMID: 38674601 PMCID: PMC11051941 DOI: 10.3390/microorganisms12040656] [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: 03/01/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Volcanic lava is an excellent model of primary succession, in which basalt-associated microorganisms drive the cycling of different elements such as nitrogen, carbon, and other nutrients. Microbial communities in volcanic soils are of particular interest for study on the emergence and evolution of life within special and extreme conditions. The initial processes of colonization and subsequent rock weathering by microbial communities are still poorly understood. We analyzed the soil bacterial and fungal communities and diversities associated with lava (LBL) and kipuka (BK) sites in Wudalianchi using 16S and ITS rRNA Illumina Miseq sequencing techniques. The results showed that soil physical and chemical properties (pH, MC, TOC, TN, TP, AP, DOC, and DON) significantly differed between LBL and BK. The Shannon, Ace, and Pd indexes of fungi in the two sites showed a significant difference (p < 0.05). The dominant bacterial phyla forming communities at LBL and BK sites were Acidobacteria, Proteobacteria, Actinobacteria, and Basidiomycota, and their differences were driven by Gemmatimonadetes and Verrucomicrobia. The dominant fungal phyla of LBL and BK sites were Ascomycota, Zygomycota, and Rozellomcota, which differed significantly between the two sites. The microbial communities showed extremely significant differences (p < 0.05), with MC, pH, and nitrogen being the main influencing factors according to RDA/CCA and correlation analysis. Microbial functional prediction analysis across the two sites showed that the relative abundance of advantageous functional groups was significantly different (p < 0.05). The combined results drive us to conclude that the volcanic soil differences in the deposits appear to be the main factor shaping the microbial communities in Wudalianchi (WDLC) volcanic ecosystems.
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Affiliation(s)
- Qingyang Huang
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China; (Q.H.); (F.Y.); (H.C.); (J.C.); (M.J.); (L.X.)
| | - Fan Yang
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China; (Q.H.); (F.Y.); (H.C.); (J.C.); (M.J.); (L.X.)
| | - Hongjie Cao
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China; (Q.H.); (F.Y.); (H.C.); (J.C.); (M.J.); (L.X.)
| | - Jiahui Cheng
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China; (Q.H.); (F.Y.); (H.C.); (J.C.); (M.J.); (L.X.)
| | - Mingyue Jiang
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China; (Q.H.); (F.Y.); (H.C.); (J.C.); (M.J.); (L.X.)
| | - Maihe Li
- Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research, CH-8903 Birmensdorf, Switzerland;
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun 130024, China
- School of Life Science, Hebei University, Baoding 071002, China
| | - Hongwei Ni
- Heilongjiang Academy of Forestry, Harbin 150040, China
| | - Lihong Xie
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China; (Q.H.); (F.Y.); (H.C.); (J.C.); (M.J.); (L.X.)
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Liu B, Zheng Y, Wang X, Qi L, Zhou J, An Z, Wu L, Chen F, Lin Z, Yin G, Dong H, Li X, Liang X, Han P, Liu M, Hou L. Active dark carbon fixation evidenced by 14C isotope assimilation and metagenomic data across the estuarine-coastal continuum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169833. [PMID: 38190922 DOI: 10.1016/j.scitotenv.2023.169833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/24/2023] [Accepted: 12/30/2023] [Indexed: 01/10/2024]
Abstract
Estuaries, as important land-ocean transitional zones across the Earth's surface, are hotspots of microbially driven dark carbon fixation (DCF), yet understanding of DCF process remains limited across the estuarine-coastal continuum. This study explored DCF activities and associated chemoautotrophs along the estuarine and coastal environmental gradients, using radiocarbon labelling and molecular techniques. Significantly higher DCF rates were observed at middle- and high-salinity regions (0.65-2.31 and 0.66-2.82 mmol C m-2 d-1, respectively), compared to low-salinity zone (0.07-0.19 mmol C m-2 d-1). Metagenomic analysis revealed relatively stable DCF pathways along the estuarine-coastal continuum, primarily dominated by Calvin-Benson-Bassham (CBB) cycle and Wood-Ljungdahl (WL) pathway. Nevertheless, chemoautotrophic communities driving DCF exhibited significant spatial variations. It is worth noting that although CBB cycle played an important role in DCF in estuarine sediments, WL pathway might play a more significant role, which has not been previously recognized. Overall, this study highlights that DCF activities coincide with the genetic potential of chemoautotrophy and the availability of reductive substrates across the estuarine-coastal continuum, and provides an important scientific basis for accurate quantitative assessment of global estuarine carbon sink.
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Affiliation(s)
- Bolin Liu
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Xinyu Wang
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lin Qi
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jie Zhou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zhirui An
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Li Wu
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Feiyang Chen
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zhuke Lin
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiaofei Li
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Ping Han
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
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11
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Samylina OS, Kosyakova AI, Krylov AA, Sorokin DY, Pimenov NV. Salinity-induced succession of phototrophic communities in a southwestern Siberian soda lake during the solar activity cycle. Heliyon 2024; 10:e26120. [PMID: 38404883 PMCID: PMC10884861 DOI: 10.1016/j.heliyon.2024.e26120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/09/2023] [Accepted: 02/07/2024] [Indexed: 02/27/2024] Open
Abstract
A variety of lakes located in the dry steppe area of southwestern Siberia are exposed to rapid climatic changes, including intra-century cycles with alternating dry and wet phases driven by solar activity. As a result, the salt lakes of that region experience significant fluctuations in water level and salinity, which have an essential impact on the indigenous microbial communities. But there are few microbiological studies that have analyzed this impact, despite its importance for understanding the functioning of regional water ecosystems. This work is a retrospective study aimed at analyzing how solar activity-related changes in hydrological regime affect phototrophic microbial communities using the example of the shallow soda lake Tanatar VI, located in the Kulunda steppe (Altai Region, Russia, southwestern Siberia). The main approach used in this study was the comparison of hydrochemical and microscopic data obtained during annual field work with satellite and solar activity data for the 12-year observation period (2011-2022). The occurrence of 33 morphotypes of cyanobacteria, two key morphotypes of chlorophytes, and four morphotypes of anoxygenic phototrophic bacteria was analyzed due to their easily recognizable morphology. During the study period, the lake surface changed threefold and the salinity changed by more than an order of magnitude, which strongly correlated with the phases of the solar activity cycles. The periods of high (2011-2014; 100-250 g/L), medium (2015-2016; 60 g/L), extremely low (2017-2020; 13-16 g/L), and low (2021-2022; 23-34 g/L) salinity with unique biodiversity of phototrophic communities were distinguished. This study shows that solar activity cycles determine the dynamics of the total salinity of a southwestern Siberian soda lake, which in turn determines the communities and microorganisms that will occur in the lake, ultimately leading to cyclical changes in alternative states of the ecosystem (dynamic stability).
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Affiliation(s)
- Olga S. Samylina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7-2, Moscow, 117312, Russia
| | - Anastasia I. Kosyakova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7-2, Moscow, 117312, Russia
- Faculty of Soil Science, Moscow State University, GSP-1, 1-12 Leninskie Gory, Moscow 119991, Russia
| | - Artem A. Krylov
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Nakhimovskiy Prospekt, 36, 117997 Moscow, Russia
| | - Dimitry Yu. Sorokin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7-2, Moscow, 117312, Russia
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Nikolay V. Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7-2, Moscow, 117312, Russia
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12
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Banchi E, Corre E, Del Negro P, Celussi M, Malfatti F. Genome-resolved metagenomics of Venice Lagoon surface sediment bacteria reveals high biosynthetic potential and metabolic plasticity as successful strategies in an impacted environment. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:126-142. [PMID: 38433960 PMCID: PMC10902248 DOI: 10.1007/s42995-023-00192-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 09/05/2023] [Indexed: 03/05/2024]
Abstract
Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from 'omics' approaches. Here, we characterized metagenome-assembled-genomes (MAGs) from the surface sediment microbes of the Venice Lagoon (northern Adriatic Sea) in distinct sub-basins exposed to various natural and anthropogenic pressures. MAGs were explored for biodiversity, major marine metabolic processes, anthropogenic activity-related functions, adaptations at the microscale, and biosynthetic gene clusters. Starting from 126 MAGs, a non-redundant dataset of 58 was compiled, the majority of which (35) belonged to (Alpha- and Gamma-) Proteobacteria. Within the broad microbial metabolic repertoire (including C, N, and S metabolisms) the potential to live without oxygen emerged as one of the most important features. Mixotrophy was also found as a successful lifestyle. Cluster analysis showed that different MAGs encoded the same metabolic patterns (e.g., C fixation, sulfate oxidation) thus suggesting metabolic redundancy. Antibiotic and toxic compounds resistance genes were coupled, a condition that could promote the spreading of these genetic traits. MAGs showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular detoxification. Our results highlighted that bacteria living in an impacted environment, such as the surface sediments of the Venice Lagoon, may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites, promoting ecosystem resilience and stability toward environmental pressures. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00192-z.
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Affiliation(s)
- Elisa Banchi
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Erwan Corre
- FR2424, Station Biologique de Roscoff, Plateforme ABiMS (Analysis and Bioinformatics for Marine Science), Sorbonne Université CNRS, 29680 Roscoff, France
| | - Paola Del Negro
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Francesca Malfatti
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
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13
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Zhao D, Zhang S, Chen J, Zhao J, An P, Xiang H. Members of the class Candidatus Ordosarchaeia imply an alternative evolutionary scenario from methanogens to haloarchaea. THE ISME JOURNAL 2024; 18:wrad033. [PMID: 38366248 PMCID: PMC10873845 DOI: 10.1093/ismejo/wrad033] [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: 10/08/2023] [Revised: 12/05/2023] [Accepted: 12/19/2023] [Indexed: 02/18/2024]
Abstract
The origin of methanogenesis can be traced to the common ancestor of non-DPANN archaea, whereas haloarchaea (or Halobacteria) are believed to have evolved from a methanogenic ancestor through multiple evolutionary events. However, due to the accelerated evolution and compositional bias of proteins adapting to hypersaline habitats, Halobacteria exhibit substantial evolutionary divergence from methanogens, and the identification of the closest methanogen (either Methanonatronarchaeia or other taxa) to Halobacteria remains a subject of debate. Here, we obtained five metagenome-assembled genomes with high completeness from soda-saline lakes on the Ordos Plateau in Inner Mongolia, China, and we proposed the name Candidatus Ordosarchaeia for this novel class. Phylogenetic analyses revealed that Ca. Ordosarchaeia is firmly positioned near the median position between the Methanonatronarchaeia and Halobacteria-Hikarchaeia lineages. Functional predictions supported the transitional status of Ca. Ordosarchaeia with the metabolic potential of nonmethanogenic and aerobic chemoheterotrophy, as did remnants of the gene sequences of methylamine/dimethylamine/trimethylamine metabolism and coenzyme M biosynthesis. Based on the similarity of the methyl-coenzyme M reductase genes mcrBGADC in Methanonatronarchaeia with the phylogenetically distant methanogens, an alternative evolutionary scenario is proposed, in which Methanonatronarchaeia, Ca. Ordosarchaeia, Ca. Hikarchaeia, and Halobacteria share a common ancestor that initially lost mcr genes. However, certain members of Methanonatronarchaeia subsequently acquired mcr genes through horizontal gene transfer from distantly related methanogens. This hypothesis is supported by amalgamated likelihood estimation, phylogenetic analysis, and gene arrangement patterns. Altogether, Ca. Ordosarchaeia genomes clarify the sisterhood of Methanonatronarchaeia with Halobacteria and provide new insights into the evolution from methanogens to haloarchaea.
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Affiliation(s)
- Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengjie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Junyu Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Juanjuan Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng An
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, Sichuan Normal University, Sichuan 610068, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
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14
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Man DKW, Hermans SM, Taubert M, Garcia SL, Hengoju S, Küsel K, Rosenbaum MA. Enrichment of different taxa of the enigmatic candidate phyla radiation bacteria using a novel picolitre droplet technique. ISME COMMUNICATIONS 2024; 4:ycae080. [PMID: 38946848 PMCID: PMC11214157 DOI: 10.1093/ismeco/ycae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/24/2024] [Accepted: 06/20/2024] [Indexed: 07/02/2024]
Abstract
The candidate phyla radiation (CPR) represents a distinct monophyletic clade and constitutes a major portion of the tree of life. Extensive efforts have focused on deciphering the functional diversity of its members, primarily using sequencing-based techniques. However, cultivation success remains scarce, presenting a significant challenge, particularly in CPR-dominated groundwater microbiomes characterized by low biomass. Here, we employ an advanced high-throughput droplet microfluidics technique to enrich CPR taxa from groundwater. Utilizing a low-volume filtration approach, we successfully harvested a microbiome resembling the original groundwater microbial community. We assessed CPR enrichment in droplet and aqueous bulk cultivation for 30 days using a novel CPR-specific primer to rapidly track the CPR fraction through the cultivation attempts. The combination of soil extract and microbial-derived necromass provided the most supportive conditions for CPR enrichment. Employing these supplemented conditions, droplet cultivation proved superior to bulk cultivation, resulting in up to a 13-fold CPR enrichment compared to a 1- to 2-fold increase in bulk cultivation. Amplicon sequencing revealed 10 significantly enriched CPR orders. The highest enrichment in CPRs was observed for some unknown members of the Parcubacteria order, Cand. Jorgensenbacteria, and unclassified UBA9983. Furthermore, we identified co-enriched putative host taxa, which may guide more targeted CPR isolation approaches in subsequent investigations.
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Affiliation(s)
- DeDe Kwun Wai Man
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), 07745 Jena, Germany
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
| | - Syrie M Hermans
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
- Food Science and Microbiology, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, 1142 Auckland, New Zealand
- Aquatic Geomicrobiology, Institute of Biodiversity, Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
| | - Martin Taubert
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
- Aquatic Geomicrobiology, Institute of Biodiversity, Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, 106 91 Stockholm, Sweden
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg, Germany
| | - Sundar Hengoju
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), 07745 Jena, Germany
| | - Kirsten Küsel
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
- Aquatic Geomicrobiology, Institute of Biodiversity, Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Miriam A Rosenbaum
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), 07745 Jena, Germany
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
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15
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Modolon F, Schultz J, Duarte G, Vilela CLS, Thomas T, Peixoto RS. In situ devices can culture the microbial dark matter of corals. iScience 2023; 26:108374. [PMID: 38162026 PMCID: PMC10755713 DOI: 10.1016/j.isci.2023.108374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/16/2023] [Accepted: 10/27/2023] [Indexed: 01/03/2024] Open
Abstract
Most microorganisms found in environmental samples have never been cultured and can often only be explored through molecular or microscopic approaches. Here, we adapt the use of in situ diffusion-based devices to culture "yet-to-be-cultured" microorganisms associated with coral mucus and compare this with a traditional culturing method. The culturability of microorganisms associated with mucus of the coral Pocillopora damicornis increased by 420% and 570% with diffusion growth chambers and microwell chip devices, respectively, compared with the traditional method tested. The obtained cultures represent up to 64.4% of the total diversity of amplicon sequence variants (ASVs) found in the mucus of the coral P. damicornis. In addition, some previously uncultured microorganisms, such as members of the family Nitrosopumilaceae and halophilic/halotolerant bacteria were cultured. Our results validate alternative microbial culturing strategies to culture coral-associated microorganisms, while significantly increasing the culturability of previous microbial dark matter.
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Affiliation(s)
- Flúvio Modolon
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Júnia Schultz
- King Abdullah University of Science and Technology (KAUST), Marine Science and Bioscience Programs, Red Sea Research Center (RSRC) and Computational Biology Center (CBRC), Environmental and Engineering Sciences Division (BESE Thuwal, Makkah 23955, Saudi Arabia
| | - Gustavo Duarte
- King Abdullah University of Science and Technology (KAUST), Marine Science and Bioscience Programs, Red Sea Research Center (RSRC) and Computational Biology Center (CBRC), Environmental and Engineering Sciences Division (BESE Thuwal, Makkah 23955, Saudi Arabia
| | - Caren Leite Spindola Vilela
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Raquel Silva Peixoto
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- King Abdullah University of Science and Technology (KAUST), Marine Science and Bioscience Programs, Red Sea Research Center (RSRC) and Computational Biology Center (CBRC), Environmental and Engineering Sciences Division (BESE Thuwal, Makkah 23955, Saudi Arabia
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16
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Font-Verdera F, Liébana R, Rossello-Mora R, Viver T. Impact of dilution on stochastically driven methanogenic microbial communities of hypersaline anoxic sediments. FEMS Microbiol Ecol 2023; 99:fiad146. [PMID: 37989854 PMCID: PMC10673710 DOI: 10.1093/femsec/fiad146] [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: 04/27/2023] [Revised: 10/02/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023] Open
Abstract
Sediments underlying the solar salterns of S'Avall are anoxic hypersaline ecosystems dominated by anaerobic prokaryotes, and with the especial relevance of putative methanogenic archaea. Slurries from salt-saturated sediments, diluted in a gradient of salinity and incubated for > 4 years revealed that salt concentration was the major selection force that deterministically structured microbial communities. The dominant archaea in the original communities showed a decrease in alpha diversity with dilution accompanied by the increase of bacterial alpha diversity, being highest at 5% salts. Correspondingly, methanogens decreased and in turn sulfate reducers increased with decreasing salt concentrations. Methanogens especially dominated at 25%. Different concentrations of litter of Posidonia oceanica seagrass added as a carbon substrate, did not promote any clear relevant effect. However, the addition of ampicillin as selection pressure exerted important effects on the assemblage probably due to the removal of competitors or enhancers. The amended antibiotic enhanced methanogenesis in the concentrations ≤ 15% of salts, whereas it was depleted at salinities ≥ 20% revealing key roles of ampicillin-sensitive bacteria.
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Affiliation(s)
- Francisca Font-Verdera
- Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marquès, 21, 07190 Esporles, Illes Balears, SPAIN
| | - Raquel Liébana
- Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marquès, 21, 07190 Esporles, Illes Balears, SPAIN
- AZTI, Basque Research Technology Alliance (BRTA), Txatxarramendi ugartea z/g, Sukarrieta, 48395 Sukarrieta, Bizkaia, Spain
| | - Ramon Rossello-Mora
- Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marquès, 21, 07190 Esporles, Illes Balears, SPAIN
| | - Tomeu Viver
- Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marquès, 21, 07190 Esporles, Illes Balears, SPAIN
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
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17
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Wang L, Lian C, Wan W, Qiu Z, Luo X, Huang Q, Deng Y, Zhang T, Yu K. Salinity-triggered homogeneous selection constrains the microbial function and stability in lakes. Appl Microbiol Biotechnol 2023; 107:6591-6605. [PMID: 37688597 DOI: 10.1007/s00253-023-12696-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/24/2023] [Accepted: 07/18/2023] [Indexed: 09/11/2023]
Abstract
Climate change and anthropogenic exploitation have led to the gradual salinization of inland waters worldwide. However, the impacts of this process on the prokaryotic plankton communities and their role in biogeochemical cycles in the inland lake are poorly known. Here, we take a space-for-time substitution approach, using 16S rRNA gene amplicon sequencing and metagenomic sequencing. We analyzed the prokaryotic plankton communities of 11 lakes in northwest China, with average water salinities ranging from 0.002 to 14.370%. The results demonstrated that, among the various environmental parameters, salinity was the most important driver of prokaryotic plankton β-diversity (Mantel test, r = 0.53, P < 0.001). (1) Under low salinity, prokaryotic planktons were assembled by stochastic processes and employed diverse halotolerant strategies, including the synthesis and uptake of compatible solutes and extrusion of Na+ or Li+ in exchange for H+. Under elevated salinity pressure, strong homogeneous selection meant that only planktonic prokaryotes showing an energetically favorable halotolerant strategy employing an Mnh-type Na+/H+ antiporter remained. (2) The decreasing taxonomic diversity caused by intense environmental filtering in high-salinity lakes impaired functional diversity related to substance metabolism. The prokaryotes enhanced the TCA cycle, carbon fixation, and low-energy-consumption amino acid biosynthesis in high-salinity lakes. (3) Elevated salinity pressure decreased the negative:positive cohesion and the modularity of the molecular ecology networks for the planktonic prokaryotes, indicating a precarious microbial network. Our findings provide new insights into plankton ecology and are helpful for the protecting of the biodiversity and function of inland lakes against the background of salinization. KEY POINTS: • Increased salinity enhances homogeneous selection in the microbial assembly. • Elevated salinity decreases the microbial co-occurrence networks stability. • High salinity damages the microbial function diversity.
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Affiliation(s)
- Li Wang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Chunang Lian
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Zhiguang Qiu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Xuesong Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of ·Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of ·Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
| | - Ke Yu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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18
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Mujakić I, Cabello-Yeves PJ, Villena-Alemany C, Piwosz K, Rodriguez-Valera F, Picazo A, Camacho A, Koblížek M. Multi-environment ecogenomics analysis of the cosmopolitan phylum Gemmatimonadota. Microbiol Spectr 2023; 11:e0111223. [PMID: 37732776 PMCID: PMC10581226 DOI: 10.1128/spectrum.01112-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/02/2023] [Indexed: 09/22/2023] Open
Abstract
Gemmatimonadota is a diverse bacterial phylum commonly found in environments such as soils, rhizospheres, fresh waters, and sediments. So far, the phylum contains just six cultured species (five of them sequenced), which limits our understanding of their diversity and metabolism. Therefore, we analyzed over 400 metagenome-assembled genomes (MAGs) and 5 culture-derived genomes representing Gemmatimonadota from various aquatic environments, hydrothermal vents, sediments, soils, and host-associated (with marine sponges and coral) species. The principal coordinate analysis based on the presence/absence of genes in Gemmatimonadota genomes and phylogenomic analysis documented that marine and host-associated Gemmatimonadota were the most distant from freshwater and wastewater species. A smaller genome size and coding sequences (CDS) number reduction were observed in marine MAGs, pointing to an oligotrophic environmental adaptation. Several metabolic pathways are restricted to specific environments. For example, genes for anoxygenic phototrophy were found only in freshwater, wastewater, and soda lake sediment genomes. There were several genomes from soda lake sediments and wastewater containing type IC/ID ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Various genomes from wastewater harbored bacterial type II RuBisCO, whereas RuBisCO-like protein was found in genomes from fresh waters, soil, host-associated, and marine sediments. Gemmatimonadota does not contain nitrogen fixation genes; however, the nosZ gene, involved in the reduction of N2O, was present in genomes from most environments, missing only in marine water and host-associated Gemmatimonadota. The presented data suggest that Gemmatimonadota evolved as an organotrophic species relying on aerobic respiration and then remodeled its genome inventory when adapting to particular environments. IMPORTANCE Gemmatimonadota is a rarely studied bacterial phylum consisting of a handful of cultured species. Recent culture-independent studies documented that these organisms are distributed in many environments, including soil, marine, fresh, and waste waters. However, due to the lack of cultured species, information about their metabolic potential and environmental role is scarce. Therefore, we collected Gemmatimonadota metagenome-assembled genomes (MAGs) from different habitats and performed a systematic analysis of their genomic characteristics and metabolic potential. Our results show how Gemmatimonadota have adapted their genomes to different environments.
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Affiliation(s)
- Izabela Mujakić
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Pedro J. Cabello-Yeves
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Valencia, Spain
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Cristian Villena-Alemany
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Kasia Piwosz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Gdynia, Poland
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Valencia, Spain
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Valencia, Spain
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
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Boltyanskaya Y, Zhilina T, Grouzdev D, Detkova E, Pimenov N, Kevbrin V. Halanaerobium polyolivorans sp. nov.-A Novel Halophilic Alkalitolerant Bacterium Capable of Polyol Degradation: Physiological Properties and Genomic Insights. Microorganisms 2023; 11:2325. [PMID: 37764169 PMCID: PMC10536098 DOI: 10.3390/microorganisms11092325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/16/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
A search for the microorganisms responsible for the anaerobic degradation of osmoprotectants in soda lakes resulted in the isolation of a novel halophilic and alkalitolerant strain, designated Z-7514T. The cells were Gram-stain-negative and non-endospore-forming rods. Optimal growth occurs at 1.6-2.1 M Na+, pH 8.0-8.5, and 31-35 °C. The strain utilized mainly sugars, low molecular polyols, and ethanolamine as well. The G+C content of the genomic DNA of strain Z-7514T was 33.3 mol%. Phylogenetic and phylogenomic analyses revealed that strain Z-7514T belongs to the genus Halanaerobium. On the basis of phenotypic properties and the dDDH and ANI values with close validly published species, it was proposed to evolve strain Z-7514T within the genus Halanaerobium into novel species, for which the name Halanaerobium polyolivorans sp. nov. was proposed. The type strain was Z-7514T (=KCTC 25405T = VKM B-3577T). For species of the genus Halanaerobium, the utilization of ethylene glycol, propylene glycol, and ethanolamine were shown for the first time. The anaerobic degradation of glycols and ethanolamine by strain Z-7514T may represent a novel metabiotic pathway within the alkaliphilic microbial community. Based on a detailed genomic analysis, the main pathways of catabolism of most of the used substrates have been identified.
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Affiliation(s)
- Yulia Boltyanskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia; (Y.B.); (T.Z.); (E.D.); (N.P.)
| | - Tatjana Zhilina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia; (Y.B.); (T.Z.); (E.D.); (N.P.)
| | | | - Ekaterina Detkova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia; (Y.B.); (T.Z.); (E.D.); (N.P.)
| | - Nikolay Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia; (Y.B.); (T.Z.); (E.D.); (N.P.)
| | - Vadim Kevbrin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia; (Y.B.); (T.Z.); (E.D.); (N.P.)
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20
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Zavarzina DG, Merkel AY, Klyukina AA, Elizarov IM, Pikhtereva VA, Rusakov VS, Chistyakova NI, Ziganshin RH, Maslov AA, Gavrilov SN. Iron or sulfur respiration-an adaptive choice determining the fitness of a natronophilic bacterium Dethiobacter alkaliphilus in geochemically contrasting environments. Front Microbiol 2023; 14:1108245. [PMID: 37520367 PMCID: PMC10376724 DOI: 10.3389/fmicb.2023.1108245] [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: 11/25/2022] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Haloalkaliphilic microorganisms are double extremophiles functioning optimally at high salinity and pH. Their typical habitats are soda lakes, geologically ancient yet widespread ecosystems supposed to harbor relict microbial communities. We compared metabolic features and their determinants in two strains of the natronophilic species Dethiobacter alkaliphilus, the only cultured representative of the class "Dethiobacteria" (Bacillota). The strains of D. alkaliphilus were previously isolated from geographically remote Mongolian and Kenyan soda lakes. The type strain AHT1T was described as a facultative chemolithoautotrophic sulfidogen reducing or disproportionating sulfur or thiosulfate, while strain Z-1002 was isolated as a chemolithoautotrophic iron reducer. Here, we uncovered the iron reducing ability of strain AHT1T and the ability of strain Z-1002 for thiosulfate reduction and anaerobic Fe(II) oxidation. Key catabolic processes sustaining the growth of both D. alkaliphilus strains appeared to fit the geochemical settings of two contrasting natural alkaline environments, sulfur-enriched soda lakes and iron-enriched serpentinites. This hypothesis was supported by a meta-analysis of Dethiobacterial genomes and by the enrichment of a novel phylotype from a subsurface alkaline aquifer under Fe(III)-reducing conditions. Genome analysis revealed multiheme c-type cytochromes to be the most probable determinants of iron and sulfur redox transformations in D. alkaliphilus. Phylogeny reconstruction showed that all the respiratory processes in this organism are likely provided by evolutionarily related early forms of unconventional octaheme tetrathionate and sulfite reductases and their structural analogs, OmhA/OcwA Fe(III)-reductases. Several phylogenetically related determinants of anaerobic Fe(II) oxidation were identified in the Z-1002 genome, and the oxidation process was experimentally demonstrated. Proteomic profiling revealed two distinct sets of multiheme cytochromes upregulated in iron(III)- or thiosulfate-respiring cells and the cytochromes peculiar for Fe(II) oxidizing cells. We suggest that maintaining high variation in multiheme cytochromes is an effective adaptive strategy to occupy geochemically contrasting alkaline environments. We propose that sulfur-enriched soda lakes could be secondary habitats for D. alkaliphilus compared to Fe-rich serpentinites, and that the ongoing evolution of Dethiobacterales could retrace the evolutionary path that may have occurred in prokaryotes at a turning point in the biosphere's history, when the intensification of the sulfur cycle outweighed the global significance of the iron cycle.
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Affiliation(s)
- Daria G. Zavarzina
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Yu Merkel
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ivan M. Elizarov
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Valeria A. Pikhtereva
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Maslov
- Faculty of Geology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey N. Gavrilov
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
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21
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Trutschel LR, Kruger BR, Sackett JD, Chadwick GL, Rowe AR. Determining resident microbial community members and their correlations with geochemistry in a serpentinizing spring. Front Microbiol 2023; 14:1182497. [PMID: 37396382 PMCID: PMC10308030 DOI: 10.3389/fmicb.2023.1182497] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/24/2023] [Indexed: 07/04/2023] Open
Abstract
Terrestrial serpentinizing systems allow us insight into the realm of alkaliphilic microbial communities driven by geology in a way that is frequently more accessible than their deep subsurface or marine counterparts. However, these systems are also marked by geochemical and microbial community variation due to the interactions of serpentinized fluids with host geology and the surface environment. To separate the transient from the endemic microbes in a hyperalkaline environment, we assessed the Ney Springs terrestrial serpentinizing system microbial community and geochemistry at six time points over the span of a year. Using 16S rRNA gene surveys we observed 93 amplicon sequence variants (ASVs) that were found at every sampling event. This is compared to ~17,000 transient ASVs that were detected only once across the six sampling events. Of the resident community members, 16 of these ASVs were regularly greater than 1% of the community during every sampling period. Additionally, many of these core taxa experienced statistically significant changes in relative abundance with time. Variation in the abundance of some core populations correlated with geochemical variation. For example, members of the Tindallia group, showed a positive correlation with variation in levels of ammonia at the spring. Investigating the metagenome assembled genomes of these microbes revealed evidence of the potential for ammonia generation via Stickland reactions within Tindallia. This observation offers new insight into the origin of high ammonia concentrations (>70 mg/L) seen at this site. Similarly, the abundance of putative sulfur-oxidizing microbes like Thiomicrospira, Halomonas, and a Rhodobacteraceae species could be linked to changes observed in sulfur-oxidation intermediates like tetrathionate and thiosulfate. While these data supports the influence of core microbial community members on a hyperalkaline spring's geochemistry, there is also evidence that subsurface processes affect geochemistry and may impact community dynamics as well. Though the physiology and ecology of these astrobiologically relevant ecosystems are still being uncovered, this work helps identify a stable microbial community that impacts spring geochemistry in ways not previously observed in serpentinizing ecosystems.
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Affiliation(s)
- Leah R. Trutschel
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Brittany R. Kruger
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, Las Vegas, NV, United States
| | - Joshua D. Sackett
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Grayson L. Chadwick
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Annette R. Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
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22
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Liu YH, Mohamad OAA, Gao L, Xie YG, Abdugheni R, Huang Y, Li L, Fang BZ, Li WJ. Sediment prokaryotic microbial community and potential biogeochemical cycle from saline lakes shaped by habitat. Microbiol Res 2023; 270:127342. [PMID: 36848700 DOI: 10.1016/j.micres.2023.127342] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 02/23/2023]
Abstract
The microbial diversity and ecological function in different saline lakes was reduced or disappeared as the influence of climate change and human activities even before they were known. However, reports about prokaryotic microbial of saline lakes from Xinjiang are very limited especially in large-scale investigations. In this study, a total of 6 saline lakes represented three different habitats, including hypersaline lake (HSL), arid saline lake (ASL), and light saltwater lake (LSL) were involved. The distribution pattern and potential functions of prokaryotes were investigated by using the cultivation-independent method of amplicon sequencing. The results showed that Proteobacteria was the predominant community and was widely distributed in all kinds of saline lakes, Desulfobacterota was the representative community in hypersaline lakes, Firmicutes and Acidobacteriota were mainly distributed in arid saline lake samples, and Chloroflexi was more abundant in light saltwater lakes. Specifically, the archaeal community was mainly distributed in the HSL and ASL samples, whereas it was very rare in the LSL lakes. The functional group showed that fermentation was the main metabolic process of microbes in all saline lakes and covered 8 phyla, including Actinobacteriota, Bacteroidota, Desulfobacterota, Firmicutes, Halanaerobiaeota, Proteobacteria, Spirochaetota, and Verrucomicrobiota. Among the 15 functional phyla, Proteobacteria was a distinctly important community in saline lakes, as it exhibited wide functions in the biogeochemical cycle. According to the correlation of environmental factors, SO42-, Na+, CO32-, and TN were significantly affected in the microbial community from saline lakes in this study. Overall, our study provided more detailed information about microbial community composition and distribution from three different habitats of saline lakes, especially the potential functions of carbon, nitrogen, and sulfur cycles, which provided new insight for understanding the complex microbiota adapt to the extreme environment and new perspectives on evaluating microbial contributions to degraded 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 830011, PR China; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 830000 Urumqi, PR 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 830011, PR China; Department of Environmental Protection, Faculty of Environmental Agricultural Sciences, Arish University, Al-Arish 45511, Egypt
| | - 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 830011, PR China
| | - Yuan-Guo Xie
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR 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 830011, PR 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 830011, PR 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 830011, PR 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 830011, PR China.
| | - 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 830011, PR China; State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
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23
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Boltyanskaya YV, Kevbrin VV, Grouzdev DS, Detkova EN, Koziaeva VV, Novikov AA, Zhilina TN. Halonatronomonas betaini gen. nov., sp. nov., a haloalkaliphilic isolate from soda lake capable of betaine degradation and proposal of Halarsenatibacteraceae fam. nov. and Halothermotrichaceae fam. nov. within the order Halanaerobiales. Syst Appl Microbiol 2023; 46:126407. [PMID: 36906934 DOI: 10.1016/j.syapm.2023.126407] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 02/11/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
A search for the organisms responsible for anaerobic betaine degradation in soda lakes resulted in isolation of a novel bacterial strain, designated Z-7014T. The cells were Gram-stain-negative, non-endospore-forming rods. Growth occurred at 8-52 °C (optimum 40-45 °C), pH 7.1-10.1 (optimum pH 8.1-8.8) and 1.0-3.5 M Na+ (optimum 1.8 M), i.e. it can be regarded as a haloalkaliphile. The strain utilized a limited range of substrates, mostly peptonaceous but not amino acids, and was able to degrade betaine. Growth on betaine occurred only in the presence of peptonaceous substances which could not be replaced by vitamins. The G + C content of the genomic DNA of strain Z-7014T was 36.1 mol%. The major cellular fatty acids (>5% of the total) were C16:0 DMA, C18: 0 DMA, C16:1ω8, C16:0, C18:1 DMA, C16:1 DMA, C18:1ω9, and C18:0. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain Z-7014T formed a distinct evolutionary lineage in the order Halanaerobiales with the highest similarity to Halarsenitibacter silvermanii SLAS-1T (83.6%), Halothermothrix orenii H168T (85.6%), and Halocella cellulosilytica DSM 7362T (85.6%). AAI and POCP values between strain Z-7014T and type strains of the order Halanaerobiales were 51.7-57.8%, and 33.8-58.3%, respectively. Based on polyphasic results including phylogenomic data, the novel strain could be distinguished from other genera, which suggests that strain Z-7014T represents a novel species of a new genus, for which the name Halonatronomonas betaini gen. nov., sp. nov. is proposed. The type strain is Z-7014T (=KCTC 25237T = VKM B-3506T). On the basis of phylogenomic data, it is also proposed to evolve two novel families Halarsenitibacteraceae fam. nov. and Halothermotrichaceae fam. nov. within the current order Halanaerobiales.
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Affiliation(s)
- Yulia V Boltyanskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia
| | - Vadim V Kevbrin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia.
| | | | - Ekaterina N Detkova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia
| | - Veronika V Koziaeva
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia
| | | | - Tatjana N Zhilina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia
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24
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Maltsev A, Zelenina D, Safonov A. Microbial Diversity and Authigenic Mineral Formation of Modern Bottom Sediments in the Littoral Zone of Lake Issyk-Kul, Kyrgyz Republic (Central Asia). BIOLOGY 2023; 12:642. [PMID: 37237455 PMCID: PMC10215221 DOI: 10.3390/biology12050642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023]
Abstract
This article presents geochemical, mineralogical and microbiological characteristics of five samples of modern bottom sediments in the littoral zone of the high-mountain salty lake Issyk-Kul. The 16S rRNA gene sequencing method shows that the microbial community consists of organic carbon degraders (representatives of phyla: Proteobacteria, Chloroflexi, Bacteroidota and Verrucomicrobiota and families Anaerolineaceae and Hungateiclostridiaceae), photosynthetic microorganisms (representatives of Chloroflexi, phototrophic Acidobacteria, purple sulphur bacteria Chromatiaceae and cyanobacteria) and bacteria of the reducing branches of the sulphur biogeochemical cycle (representatives of Desulfobacterota, Desulfosarcinaceae and Desulfocapsaceae). The participation of microorganisms in processes in the formation of a number of authigenic minerals (calcite, framboidal pyrite, barite and amorphous Si) is established. The high diversity of microbial communities indicates the presence of labile organic components involved in modern biogeochemical processes in sediments. The active destruction of organic matter begins at the water-sediment interface.
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Affiliation(s)
- Anton Maltsev
- V.S. Sobolev Institute of Geology and Mineralogy Siberian Branch, RAS, Novosibirsk 630090, Russia
| | - Darya Zelenina
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia
| | - Alexey Safonov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia
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Pellegrinetti TA, Cotta SR, Sarmento H, Costa JS, Delbaje E, Montes CR, Camargo PB, Barbiero L, Rezende-Filho AT, Fiore MF. Bacterial Communities Along Environmental Gradients in Tropical Soda Lakes. MICROBIAL ECOLOGY 2023; 85:892-903. [PMID: 35916937 DOI: 10.1007/s00248-022-02086-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 07/25/2022] [Indexed: 05/04/2023]
Abstract
Soda lake environments are known to be variable and can have distinct differences according to geographical location. In this study, we investigated the effects of different environmental conditions of six adjacent soda lakes in the Pantanal biome (Mato Grosso do Sul state, Brazil) on bacterial communities and their functioning using a metagenomic approach combined with flow cytometry and chemical analyses. Ordination analysis using flow cytometry and water chemistry data from two sampling periods (wet and dry) clustered soda lakes into three different profiles: eutrophic turbid (ET), oligotrophic turbid (OT), and clear vegetated oligotrophic (CVO). Analysis of bacterial community composition and functioning corroborated this ordination; the exception was one ET lake, which was similar to one OT lake during the wet season, indicating drastic shifts between seasons. Microbial abundance and diversity increased during the dry period, along with a considerable number of limnological variables, all indicative of a strong effect of the precipitation-evaporation balance in these systems. Cyanobacteria were associated with high electric conductivity, pH, and nutrient availability, whereas Actinobacteria, Alphaproteobacteria, and Betaproteobacteria were correlated with landscape morphology variability (surface water, surface perimeter, and lake volume) and with lower salinity and pH levels. Stress response metabolism was enhanced in OT and ET lakes and underrepresented in CVO lakes. The microbiome dataset of this study can serve as a baseline for restoring impacted soda lakes. Altogether, the results of this study demonstrate the sensitivity of tropical soda lakes to climate change, as slight changes in hydrological regimes might produce drastic shifts in community diversity.
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Affiliation(s)
- Thierry A Pellegrinetti
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba, São Paulo, 13416-000, Brazil
| | - Simone R Cotta
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba, São Paulo, 13416-000, Brazil
| | - Hugo Sarmento
- Department of Hydrobiology, Federal University of São Carlos (UFSCar), São Carlos, São Paulo, 13565-905, Brazil
| | - Juliana S Costa
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba, São Paulo, 13416-000, Brazil
| | - Endrews Delbaje
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba, São Paulo, 13416-000, Brazil
| | - Celia R Montes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba, São Paulo, 13416-000, Brazil
| | - Plinio B Camargo
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba, São Paulo, 13416-000, Brazil
| | - Laurent Barbiero
- The Observatory Midi-Pyrénées, Geoscience Environment Toulouse, Research Institute for Development, The National Center for Research Scientific, Paul Sabatier University, 31400, Toulouse, France
| | - Ary T Rezende-Filho
- Faculty of Engineering, Architecture and Urbanism and Geography, Federal University of Mato Grosso do Sul, Mato Grosso do Sul, Campo Grande, 79070-900, Brazil
| | - Marli F Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba, São Paulo, 13416-000, Brazil.
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Albright S, Louca S. Trait biases in microbial reference genomes. Sci Data 2023; 10:84. [PMID: 36759614 PMCID: PMC9911409 DOI: 10.1038/s41597-023-01994-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.
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Affiliation(s)
- Sage Albright
- Department of Biology, University of Oregon, Eugene, USA
| | - Stilianos Louca
- Department of Biology, University of Oregon, Eugene, USA. .,Institute of Ecology and Evolution, University of Oregon, Eugene, USA.
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Galisteo C, de la Haba RR, Sánchez-Porro C, Ventosa A. Biotin pathway in novel Fodinibius salsisoli sp. nov., isolated from hypersaline soils and reclassification of the genus Aliifodinibius as Fodinibius. Front Microbiol 2023; 13:1101464. [PMID: 36777031 PMCID: PMC9909488 DOI: 10.3389/fmicb.2022.1101464] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/22/2022] [Indexed: 01/27/2023] Open
Abstract
Hypersaline soils are extreme environments that have received little attention until the last few years. Their halophilic prokaryotic population seems to be more diverse than those of well-known aquatic systems. Among those inhabitants, representatives of the family Balneolaceae (phylum Balneolota) have been described to be abundant, but very few members have been isolated and characterized to date. This family comprises the genera Aliifodinibius and Fodinibius along with four others. A novel strain, designated 1BSP15-2V2T, has been isolated from hypersaline soils located in the Odiel Saltmarshes Natural Area (Southwest Spain), which appears to represent a new species related to the genus Aliifodinibius. However, comparative genomic analyses of members of the family Balneolaceae have revealed that the genera Aliifodinibius and Fodinibius belong to a single genus, hence we propose the reclassification of the species of the genus Aliifodinibius into the genus Fodinibius, which was first described. The novel strain is thus described as Fodinibius salsisoli sp. nov., with 1BSP15-2V2T (=CCM 9117T = CECT 30246T) as the designated type strain. This species and other closely related ones show abundant genomic recruitment within 80-90% identity range when searched against several hypersaline soil metagenomic databases investigated. This might suggest that there are still uncultured, yet abundant closely related representatives to this family present in these environments. In-depth in-silico analysis of the metabolism of Fodinibius showed that the biotin biosynthesis pathway was present in the genomes of strain 1BSP15-2V2T and other species of the family Balneolaceae, which could entail major implications in their community role providing this vitamin to other organisms that depend on an exogenous source of this nutrient.
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Coskun ÖK, Gomez-Saez GV, Beren M, Ozcan D, Hosgormez H, Einsiedl F, Orsi WD. Carbon metabolism and biogeography of candidate phylum " Candidatus Bipolaricaulota" in geothermal environments of Biga Peninsula, Turkey. Front Microbiol 2023; 14:1063139. [PMID: 36910224 PMCID: PMC9992828 DOI: 10.3389/fmicb.2023.1063139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/17/2023] [Indexed: 02/25/2023] Open
Abstract
Terrestrial hydrothermal springs and aquifers are excellent sites to study microbial biogeography because of their high physicochemical heterogeneity across relatively limited geographic regions. In this study, we performed 16S rRNA gene sequencing and metagenomic analyses of the microbial diversity of 11 different geothermal aquifers and springs across the tectonically active Biga Peninsula (Turkey). Across geothermal settings ranging in temperature from 43 to 79°C, one of the most highly represented groups in both 16S rRNA gene and metagenomic datasets was affiliated with the uncultivated phylum "Candidatus Bipolaricaulota" (former "Ca. Acetothermia" and OP1 division). The highest relative abundance of "Ca. Bipolaricaulota" was observed in a 68°C geothermal brine sediment, where it dominated the microbial community, representing 91% of all detectable 16S rRNA genes. Correlation analysis of "Ca. Bipolaricaulota" operational taxonomic units (OTUs) with physicochemical parameters indicated that salinity was the strongest environmental factor measured associated with the distribution of this novel group in geothermal fluids. Correspondingly, analysis of 23 metagenome-assembled genomes (MAGs) revealed two distinct groups of "Ca. Bipolaricaulota" MAGs based on the differences in carbon metabolism: one group encoding the bacterial Wood-Ljungdahl pathway (WLP) for H2 dependent CO2 fixation is selected for at lower salinities, and a second heterotrophic clade that lacks the WLP that was selected for under hypersaline conditions in the geothermal brine sediment. In conclusion, our results highlight that the biogeography of "Ca. Bipolaricaulota" taxa is strongly correlated with salinity in hydrothermal ecosystems, which coincides with key differences in carbon acquisition strategies. The exceptionally high relative abundance of apparently heterotrophic representatives of this novel candidate Phylum in geothermal brine sediment observed here may help to guide future enrichment experiments to obtain representatives in pure culture.
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Affiliation(s)
- Ömer K Coskun
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gonzalo V Gomez-Saez
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Murat Beren
- Department of Geological Engineering, Istanbul University-Cerrahpasa, Istanbul, Türkiye
| | - Dogacan Ozcan
- Department of Geological Engineering, Istanbul University-Cerrahpasa, Istanbul, Türkiye
| | - Hakan Hosgormez
- Department of Geological Engineering, Istanbul University-Cerrahpasa, Istanbul, Türkiye
| | - Florian Einsiedl
- Chair of Hydrogeology, TUM School of Engineering and Design, Technical University of Munich, Munich, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
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Comparative Genomic Insights into the Evolution of Halobacteria-Associated " Candidatus Nanohaloarchaeota". mSystems 2022; 7:e0066922. [PMID: 36259734 PMCID: PMC9765267 DOI: 10.1128/msystems.00669-22] [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] [Indexed: 12/25/2022] Open
Abstract
Members of the phylum "Candidatus Nanohaloarchaeota," a representative lineage within the DPANN superphylum, are characterized by their nanosized cells and symbiotic lifestyle with Halobacteria. However, the development of the symbiosis remains unclear. Here, we propose two novel families, "Candidatus Nanoanaerosalinaceae" and "Candidatus Nanohalalkaliarchaeaceae" in "Ca. Nanohaloarchaeota," represented by five dereplicated metagenome-assembled genomes obtained from hypersaline sediments or related enrichment cultures of soda-saline lakes. Phylogenetic analyses reveal that the two novel families are placed at the root of the family "Candidatus Nanosalinaceae," including the cultivated taxa. The two novel families prefer hypersaline sediments, and the acid shift of predicted proteomes indicates a "salt-in" strategy for hypersaline adaptation. They contain a lower proportion of putative horizontal gene transfers from Halobacteria than "Ca. Nanosalinaceae," suggesting a weaker association with Halobacteria. Functional prediction and historical events reconstruction disclose that they exhibit divergent potentials in carbohydrate and organic acid metabolism and environmental responses. Globally, comparative genomic analyses based on the new families enrich the taxonomic and functional diversity of "Ca. Nanohaloarchaeota" and provide insights into the evolutionary process of "Ca. Nanohaloarchaeota" and their symbiotic relationship with Halobacteria. IMPORTANCE The DPANN superphylum is a group of archaea widely distributed in various habitats. They generally have small cells and have a symbiotic lifestyle with other archaea. The archaeal symbiotic interaction is vital to understanding microbial communities. However, the formation and evolution of the symbiosis between the DPANN lineages and other diverse archaea remain unclear. Based on phylogeny, habitat distribution, hypersaline adaptation, host prediction, functional potentials, and historical events of "Ca. Nanohaloarchaeota," a representative phylum within the DPANN superphylum, we report two novel families representing intermediate stages, and we infer the evolutionary process of "Ca. Nanohaloarchaeota" and their Halobacteria-associated symbiosis. Altogether, this research helps in understanding the evolution of symbiosis in "Ca. Nanohaloarchaeota" and provides a model for the evolution of other DPANN lineages.
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Zhao R, Farag IF, Jørgensen SL, Biddle JF. Occurrence, Diversity, and Genomes of " Candidatus Patescibacteria" along the Early Diagenesis of Marine Sediments. Appl Environ Microbiol 2022; 88:e0140922. [PMID: 36468881 PMCID: PMC9765117 DOI: 10.1128/aem.01409-22] [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: 08/17/2022] [Accepted: 11/14/2022] [Indexed: 12/07/2022] Open
Abstract
The phylum "Candidatus Patescibacteria" (or Candidate Phyla Radiation [CPR]) accounts for roughly one-quarter of microbial diversity on Earth, but the presence and diversity of these bacteria in marine sediments have been rarely charted. Here, we investigate the abundance, diversity, and metabolic capacities of CPR bacteria in three sediment sites (Mohns Ridge, North Pond, and Costa Rica Margin) with samples covering a wide range of redox zones formed during the early diagenesis of organic matter. Through metagenome sequencing, we found that all investigated sediment horizons contain "Ca. Patescibacteria" (0.4 to 28% of the total communities), which are affiliated with the classes "Ca. Paceibacteria," "Ca. Gracilibacteria," "Ca. Microgenomatia," "Ca. Saccharimonadia," "Ca. ABY1," and "Ca. WWE3." However, only a subset of the diversity of marine sediment "Ca. Patescibacteria," especially the classes "Ca. Paceibacteria" and "Ca. Gracilibacteria," can be captured by 16S rRNA gene amplicon sequencing with commonly used universal primers. We recovered 11 metagenome-assembled genomes (MAGs) of CPR from these sediments, most of which are novel at the family or genus level in the "Ca. Paceibacteria" class and are missed by the amplicon sequencing. While individual MAGs are confined to specific anoxic niches, the lack of capacities to utilize the prevailing terminal electron acceptors indicates that they may not be directly selected by the local redox conditions. These CPR bacteria lack essential biosynthesis pathways and may use a truncated glycolysis pathway to conserve energy as fermentative organotrophs. Our findings suggest that marine sediments harbor some novel yet widespread CPR bacteria during the early diagenesis of organic matter, which needs to be considered in population dynamics assessments in this vast environment. IMPORTANCE Ultrasmall-celled "Ca. Patescibacteria" have been estimated to account for one-quarter of the total microbial diversity on Earth, the parasitic lifestyle of which may exert a profound control on the overall microbial population size of the local ecosystems. However, their diversity and metabolic functions in marine sediments, one of the largest yet understudied ecosystems on Earth, remain virtually uncharacterized. By applying cultivation-independent approaches to a range of sediment redox zones, we reveal that "Ca. Patescibacteria" members are rare but widespread regardless of the prevailing geochemical conditions. These bacteria are affiliated with novel branches of "Ca. Patescibacteria" and have been largely missed in marker gene-based surveys. They do not have respiration capacity but may conserve energy by fermenting organic compounds from their episymbiotic hosts. Our findings suggest that these novel "Ca. Patescibacteria" are among the previously overlooked microbes in diverse marine sediments.
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Affiliation(s)
- Rui Zhao
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ibrahim F. Farag
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
| | - Steffen L. Jørgensen
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
| | - Jennifer F. Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
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31
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Navgire GS, Goel N, Sawhney G, Sharma M, Kaushik P, Mohanta YK, Mohanta TK, Al-Harrasi A. Analysis and Interpretation of metagenomics data: an approach. Biol Proced Online 2022; 24:18. [PMID: 36402995 PMCID: PMC9675974 DOI: 10.1186/s12575-022-00179-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/19/2022] [Indexed: 11/20/2022] Open
Abstract
Advances in next-generation sequencing technologies have accelerated the momentum of metagenomic studies, which is increasing yearly. The metagenomics field is one of the versatile applications in microbiology, where any interaction in the environment involving microorganisms can be the topic of study. Due to this versatility, the number of applications of this omics technology reached its horizons. Agriculture is a crucial sector involving crop plants and microorganisms interacting together. Hence, studying these interactions through the lenses of metagenomics would completely disclose a new meaning to crop health and development. The rhizosphere is an essential reservoir of the microbial community for agricultural soil. Hence, we focus on the R&D of metagenomic studies on the rhizosphere of crops such as rice, wheat, legumes, chickpea, and sorghum. These recent developments are impossible without the continuous advancement seen in the next-generation sequencing platforms; thus, a brief introduction and analysis of the available sequencing platforms are presented here to have a clear picture of the workflow. Concluding the topic is the discussion about different pipelines applied to analyze data produced by sequencing techniques and have a significant role in interpreting the outcome of a particular experiment. A plethora of different software and tools are incorporated in the automated pipelines or individually available to perform manual metagenomic analysis. Here we describe 8-10 advanced, efficient pipelines used for analysis that explain their respective workflows to simplify the whole analysis process.
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Affiliation(s)
- Gauri S Navgire
- Department of Microbiology, Savitribai Phule Pune University, Pune, Maharastra, 411007, India
| | - Neha Goel
- Department of Genetics and Tree Improvement, Forest Research Institute, 248006, Dehradun, India
| | - Gifty Sawhney
- Inflammation Pharmacology Division, Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Jammu-180001, Jammu Kashmir, India
| | - Mohit Sharma
- Department of Molecular Medicine, Medical University of Warsaw and Malopolska Center of Biotechnology, Karkow, Poland
| | | | | | - Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, 616, Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, 616, Oman.
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Li T, Yin Y. Critical assessment of pan-genomic analysis of metagenome-assembled genomes. Brief Bioinform 2022; 23:6702672. [PMID: 36124775 PMCID: PMC9677465 DOI: 10.1093/bib/bbac413] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 12/30/2022] Open
Abstract
Pan-genome analyses of metagenome-assembled genomes (MAGs) may suffer from the known issues with MAGs: fragmentation, incompleteness and contamination. Here, we conducted a critical assessment of pan-genomics of MAGs, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs. We found that incompleteness led to significant core gene (CG) loss. The CG loss remained when using different pan-genome analysis tools (Roary, BPGA, Anvi'o) and when using a mixture of MAGs and complete genomes. Contamination had little effect on core genome size (except for Roary due to in its gene clustering issue) but had major influence on accessory genomes. Importantly, the CG loss was partially alleviated by lowering the CG threshold and using gene prediction algorithms that consider fragmented genes, but to a less degree when incompleteness was higher than 5%. The CG loss also led to incorrect pan-genome functional predictions and inaccurate phylogenetic trees. Our main findings were supported by a study of real MAG-isolate genome data. We conclude that lowering CG threshold and predicting genes in metagenome mode (as Anvi'o does with Prodigal) are necessary in pan-genome analysis of MAGs. Development of new pan-genome analysis tools specifically for MAGs are needed in future studies.
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Affiliation(s)
- Tang Li
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE, 68508, USA
| | - Yanbin Yin
- Corresponding author. Yanbin Yin, Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE 68508, USA. Tel.: +1-402-472-4303; E-mail:
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Khomyakova MA, Zavarzina DG, Merkel AY, Klyukina AA, Pikhtereva VA, Gavrilov SN, Slobodkin AI. The first cultivated representatives of the actinobacterial lineage OPB41 isolated from subsurface environments constitute a novel order Anaerosomatales. Front Microbiol 2022; 13:1047580. [PMID: 36439822 PMCID: PMC9686372 DOI: 10.3389/fmicb.2022.1047580] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/24/2022] [Indexed: 08/01/2023] Open
Abstract
The continental subsurface harbors microbial populations highly enriched in uncultured taxa. OPB41 is an uncultured order-level phylogenetic lineage within the actinobacterial class Coriobacteriia. OPB41 bacteria have a wide geographical distribution, but the physiology and metabolic traits of this cosmopolitan group remain elusive. From two contrasting subsurface environments, a terrestrial mud volcano and a deep subsurface aquifer, located in the central part of Eurasia, within the Caucasus petroleum region, we have isolated two pure cultures of anaerobic actinobacteria belonging to OPB41. The cells of both strains are small non-motile rods forming numerous pili-like appendages. Strain M08DHBT is mesophilic, while strain Es71-Z0120T is a true thermophile having a broad temperature range for growth (25-77°C). Strain M08DHBT anaerobically reduces sulfur compounds and utilizes an aromatic compound 3,4-dihydroxybenzoic acid. Strain Es71-Z0120T is an obligate dissimilatory Fe(III) reducer that is unable to utilize aromatic compounds. Both isolates grow lithotrophically and consume molecular hydrogen or formate using either thiosulfate, elemental sulfur, or Fe(III) as an electron acceptor. Genomes of the strains encode the putative reductive glycine pathway for autotrophic CO2 fixation, Ni-Fe hydrogenases, putative thiosulfate/polysulfide reductases, and multiheme c-type cytochromes presumably involved in dissimilatory Fe(III) reduction. We propose to assign the isolated strains to the novel taxa of the species-order levels and describe strain M08DHBT as Anaerosoma tenue gen. nov., sp. nov., and strain Es71-Z0120T as Parvivirga hydrogeniphila gen. nov., sp. nov., being members of Anaerosomatales ord. nov. This work expands the knowledge of the diversity, metabolic functions, and ecological role of the phylum Actinomycetota.
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Affiliation(s)
- Maria A. Khomyakova
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Daria G. Zavarzina
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Y. Merkel
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Valeria A. Pikhtereva
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey N. Gavrilov
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander I. Slobodkin
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
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Sorokin DY, Merkel AY, Abbas B. Ecology of Methanonatronarchaeia. Environ Microbiol 2022; 24:5217-5229. [PMID: 35726892 PMCID: PMC9796771 DOI: 10.1111/1462-2920.16108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/19/2022] [Indexed: 01/07/2023]
Abstract
Methanonatronarchaeia represents a deep-branching phylogenetic lineage of extremely halo(alkali)philic and moderately thermophilic methyl-reducing methanogens belonging to the phylum Halobacteriota. It includes two genera, the alkaliphilic Methanonatronarchaeum and the neutrophilic Ca. Methanohalarchaeum. The former is represented by multiple closely related pure culture isolates from hypersaline soda lakes, while the knowledge about the latter is limited to a few mixed cultures with anaerobic haloarchaea. To get more insight into the distribution and ecophysiology of this enigmatic group of extremophilic methanogens, potential activity tests and enrichment cultivation with different substrates and at different conditions were performed with anaerobic sediment slurries from various hypersaline lakes in Russia. Methanonatronarchaeum proliferated exclusively in hypersaline soda lake samples mostly at elevated temperature, while at mesophilic conditions it coexisted with the extremely salt-tolerant methylotroph Methanosalsum natronophilum. Methanonatronarchaeum was also able to serve as a methylotrophic or hydrogenotrophic partner in several thermophilic enrichment cultures with fermentative bacteria. Ca. Methanohalarchaeum did not proliferate at mesophilic conditions and at thermophilic conditions it competed with extremely halophilic and moderately thermophilic methylotroph Methanohalobium, which it outcompeted at a combination of elevated temperature and methyl-reducing conditions. Overall, the results demonstrated that Methanonatronarchaeia are specialized extremophiles specifically proliferating in conditions of elevated temperature coupled with extreme salinity and simultaneous availability of a wide range of C1 -methylated compounds and H2 /formate.
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Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, Research Centre of BiotechnologyRussian Academy of SciencesMoscowRussia,Department of BiotechnologyDelft University of BiotechnologyDelftThe Netherlands
| | - Alexander Y. Merkel
- Winogradsky Institute of Microbiology, Research Centre of BiotechnologyRussian Academy of SciencesMoscowRussia
| | - Ben Abbas
- Department of BiotechnologyDelft University of BiotechnologyDelftThe Netherlands
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Abstract
Rhodopsins are widely distributed across all domains of life where they perform a plethora of functions through the conversion of electromagnetic radiation into physicochemical signals. As a result of an extensive survey of available genomic and metagenomic sequencing data, we reported the existence of novel clades and exotic sequence motifs scattered throughout the evolutionary radiations of both Type-1 and Type-3 rhodopsins that will likely enlarge the optogenetics toolbox. We expanded the typical rhodopsin blueprint by showing that a highly conserved and functionally important arginine residue (i.e., Arg82) was substituted multiple times during evolution by an extensive amino acid spectrum. We proposed the umbrella term Alt-rhodopsins (AltRs) for all such proteins that departed Arg82 orthodoxy. Some AltRs formed novel clades in the rhodopsin phylogeny and were found in giant viruses. Some newly uncovered AltRs were phylogenetically close to heliorhodopsins, which allowed a closer examination of the phylogenetic border between Type-1 rhodopsins and heliorhodopsins. Comprehensive phylogenetic trees and ancestral sequence reconstructions allowed us to advance the hypothesis that proto-heliorhodopsins were a eukaryotic innovation before their subsequent diversification into the extant Type-3 rhodopsins. IMPORTANCE The rhodopsin scaffold is remarkably versatile and widespread, coupling light availability to energy production and other light-dependent cellular responses with minor alterations to critical residues. We described an unprecedented spectrum of substitutions at one of the most conserved amino acids in the rhodopsin fold, Arg82. We denoted such phylogenetically diverse rhodopsins with the umbrella name Alt-rhodopsins (AltR) and described a distinct branch of AltRs in giant viruses. Intriguingly, some AltRs were the closest phylogenetic neighbors to Heliorhodopsins (HeRs) whose origins have remained enigmatic. Our analyses of HeR origins in the light of AltRs led us to posit a most unusual evolutionary trajectory that suggested a eukaryotic origin for HeRs before their diversification in prokaryotes.
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36
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Xie YG, Luo ZH, Fang BZ, Jiao JY, Xie QJ, Cao XR, Qu YN, Qi YL, Rao YZ, Li YX, Liu YH, Li A, Seymour C, Palmer M, Hedlund BP, Li WJ, Hua ZS. Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota. MICROBIOME 2022; 10:172. [PMID: 36242054 PMCID: PMC9563170 DOI: 10.1186/s40168-022-01376-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/22/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND Candidatus Nanohaloarchaeota, an archaeal phylum within the DPANN superphylum, is characterized by limited metabolic capabilities and limited phylogenetic diversity and until recently has been considered to exclusively inhabit hypersaline environments due to an obligate association with Halobacteria. Aside from hypersaline environments, Ca. Nanohaloarchaeota can also have been discovered from deep-subsurface marine sediments. RESULTS Three metagenome-assembled genomes (MAGs) representing a new order within the Ca. Nanohaloarchaeota were reconstructed from a stratified salt crust and proposed to represent a novel order, Nucleotidisoterales. Genomic features reveal them to be anaerobes capable of catabolizing nucleotides by coupling nucleotide salvage pathways with lower glycolysis to yield free energy. Comparative genomics demonstrated that these and other Ca. Nanohaloarchaeota inhabiting saline habitats use a "salt-in" strategy to maintain osmotic pressure based on the high proportion of acidic amino acids. In contrast, previously described Ca. Nanohaloarchaeota MAGs from geothermal environments were enriched with basic amino acids to counter heat stress. Evolutionary history reconstruction revealed that functional differentiation of energy conservation strategies drove diversification within Ca. Nanohaloarchaeota, further leading to shifts in the catabolic strategy from nucleotide degradation within deeper lineages to polysaccharide degradation within shallow lineages. CONCLUSIONS This study provides deeper insight into the ecological functions and evolution of the expanded phylum Ca. Nanohaloarchaeota and further advances our understanding on the functional and genetic associations between potential symbionts and hosts. Video Abstract.
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Affiliation(s)
- Yuan-Guo Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Zhen-Hao Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Qi-Jun Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Xing-Ru Cao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Yan-Ni Qu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yan-Lin Qi
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Yang-Zhi Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yu-Xian Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Andrew Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Cale Seymour
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, People's Republic of China.
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Syngas Fermentation to Acetate and Ethanol with Adaptative Electroactive Carboxydotrophs in Single Chambered Microbial Electrochemical System. MICROMACHINES 2022; 13:mi13070980. [PMID: 35888797 PMCID: PMC9319612 DOI: 10.3390/mi13070980] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 12/28/2022]
Abstract
Microbial electrosynthesis system (MES; single-chambered) was fabricated and evaluated with carbon cloth/graphite as a working/counter electrode employing an enriched microbiome. Continuous syngas sparging (at working electrode; WE) enabled the growth of endo electrogenic bacteria by availing the inorganic carbon source. Applied potential (−0.5 V) on the working electrode facilitated the reduction in syngas, leading to the synthesis of fatty acids and alcohols. The higher acetic acid titer of 3.8 g/L and ethanol concentration of 0.2 g/L was observed at an active microbial metabolic state, evidencing the shift in metabolism from acetogenic to solventogenesis. Voltammograms evidenced distinct redox species with low charge transfer resistance (Rct; Nyquist impedance). Reductive catalytic current (−0.02 mA) enabled the charge transfer efficiency of the cathodes favoring syngas conversion to products. The surface morphology of carbon cloth and system-designed conditions favored the growth of electrochemically active consortia. Metagenomic analysis revealed the enrichment of phylum/class with Actinobacteria, Firmicutes/Clostridia and Bacilli, which accounts for the syngas fermentation through suitable gene loci.
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Gregson BH, Bani A, Steinfield L, Holt D, Whitby C. Anaerobes and methanogens dominate the microbial communities in water harvesting ponds used by Kenyan rural smallholder farmers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 819:153040. [PMID: 35026246 DOI: 10.1016/j.scitotenv.2022.153040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Many rural smallholder farmers in Kenya use water-harvesting ponds, to collect rainwater, as sustainable sources of water for domestic and agricultural purposes. There is currently limited information regarding the microbial ecology in these ponds. Here, we used High Throughput Sequencing (HTS) to characterize the microorganisms present (including potential pathogens and indicator species) alongside ion chromatography to measure water chemistry (anion and cation concentration). Fluoride and magnesium concentration were the strongest predictor variables of the microbial community. Obligately or facultatively anaerobic bacterial genera (e.g. Spirochaeta and Opitutus) were abundant within the bacterial community, whilst Woesearchaeota and methanogens dominated the archaeal community. This suggests the water in the ponds is hypoxic or anoxic, and if used for irrigation, may potentially impact crop yield and viability. In addition, the opportunistic pathogen non-tuberculous mycobacteria (NTM), Mycobacterium fortuitum was found, comprising >1% of the bacterial community, suggesting a potential human health risk. Here we suggest low-cost changes to pond management, to improve or ameliorate pond anoxia and remove pathogens to benefit the livelihoods and welfare of these farms. This study also shows the applicability of HTS to broadly screen the microbial communities, assess water quality, and identify potentially pathogenic groups.
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Affiliation(s)
- Benjamin H Gregson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Alessia Bani
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | | | - Diane Holt
- Center for Enterprise and Entrepreneurship, Leeds University Business School, Leeds LS2 9JT, UK
| | - Corinne Whitby
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
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39
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Zhou H, Zhao D, Zhang S, Xue Q, Zhang M, Yu H, Zhou J, Li M, Kumar S, Xiang H. Metagenomic insights into the environmental adaptation and metabolism of Candidatus Haloplasmatales, one archaeal order thriving in saline lakes. Environ Microbiol 2022; 24:2239-2258. [PMID: 35048500 DOI: 10.1111/1462-2920.15899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/06/2021] [Indexed: 02/01/2023]
Abstract
The KTK 4A-related Thermoplasmata thrives in the sediment of saline lakes; however, systematic research on its taxonomy, environmental adaptation and metabolism is lacking. Here, we detected this abundant lineage in the sediment of five artificially separated ponds (salinity 7.0%-33.0%) within a Chinese soda-saline lake using culture-independent metagenomics and archaeal 16S rRNA gene amplicons. The phylogenies based on the 16S rRNA gene, and 122 archaeal ubiquitous single-copy proteins and genome-level identity analyses among the metagenome-assembled genomes demonstrate this lineage forming a novel order, Candidatus Haloplasmatales, comprising four genera affiliated with the identical family. Isoelectric point profiles of predicted proteomes suggest that most members adopt the energetically favourable 'salt-in' strategy. Functional prediction indicates the lithoheterotrophic nature with the versatile metabolic potentials for carbohydrate and organic acids as well as carbon monoxide and hydrogen utilization. Additionally, hydrogenase genes hdrABC-mvhADG are linked with incomplete reductive citrate cycle genes in the genomes, suggesting their functional connection. Comparison with the coupling of HdrABC-MvhADG and methanogenesis pathway provides new insights into the compatibility of laterally acquired methanogenesis with energy metabolism in the related order Methanomassiliicoccales. Globally, our research sheds light on the taxonomy, environmental adaptative mechanisms, metabolic potentials and evolutional significance of Ca. Haloplasmatales.
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Affiliation(s)
- Heng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shengjie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qiong Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Manqi Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Haiying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Sumit Kumar
- Enzyme and Microbial Biochemistry Lab, Department of Chemistry, Indian Institute of Technology, Delhi, India
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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Bryanskaya AV, Shipova AA, Rozanov AS, Kolpakova OA, Lazareva EV, Uvarova YE, Efimov VM, Zhmodik SM, Taran OP, Goryachkovskaya TN, Peltek SE. Diversity and Metabolism of Microbial Communities in a Hypersaline Lake along a Geochemical Gradient. BIOLOGY 2022; 11:biology11040605. [PMID: 35453804 PMCID: PMC9031644 DOI: 10.3390/biology11040605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022]
Abstract
In the south of western Siberia (Russia), there are many unique and unexplored soda, saline, and freshwater lakes. In this study, the results are presented on microbial diversity, its metabolic potential, and their relation with a set of geochemical parameters for a hypersaline lake ecosystem in the Novosibirsk region (Oblast). The metagenomic approach used in this work allowed us to determine the composition and structure of a floating microbial community, the upper layer of silt, and the strata of bottom sediments in a natural saline lake via two bioinformatic approaches, whose results are in good agreement with each other. In the floating microbial community and in the upper layers of the bottom sediment, bacteria of the Proteobacteria (Gammaproteobacteria), Cyanobacteria, and Bacteroidetes phyla were found to predominate. The lower layers were dominated by Proteobacteria (mainly Deltaproteobacteria), Gemmatimonadetes, Firmicutes, and Archaea. Metabolic pathways were reconstructed to investigate the metabolic potential of the microbial communities and other hypothetical roles of the microbial communities in the biogeochemical cycle. Relations between different taxa of microorganisms were identified, as was their potential role in biogeochemical transformations of C, N, and S in a comparative structural analysis that included various ecological niches.
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Affiliation(s)
- Alla V. Bryanskaya
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Correspondence: or ; Tel.: +7-383-363-4963 (ext. 4120)
| | - Aleksandra A. Shipova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Alexei S. Rozanov
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Oxana A. Kolpakova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Elena V. Lazareva
- V.S. Sobolev Institute of Geology and Mineralogy SB RAS, 630090 Novosibirsk, Russia; (E.V.L.); (S.M.Z.)
| | - Yulia E. Uvarova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Vadim M. Efimov
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Sergey M. Zhmodik
- V.S. Sobolev Institute of Geology and Mineralogy SB RAS, 630090 Novosibirsk, Russia; (E.V.L.); (S.M.Z.)
| | - Oxana P. Taran
- FRC Krasnoyarsk Science Center SB RAS, Institute of Chemistry and Chemical Technology SB RAS, 660036 Krasnoyarsk, Russia;
| | - Tatyana N. Goryachkovskaya
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Sergey E. Peltek
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
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Deng C, Zhao R, Qiu Z, Li B, Zhang T, Guo F, Mu R, Wu Y, Qiao X, Zhang L, Cheng JJ, Ni J, Yu K. Genome-centric metagenomics provides new insights into the microbial community and metabolic potential of landfill leachate microbiota. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151635. [PMID: 34774959 DOI: 10.1016/j.scitotenv.2021.151635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Landfills are important sources of microorganisms associated with anaerobic digestion. However, the knowledge on microbiota along with their functional potential in this special habitat are still lacking. In this study, we recovered 1168 non-redundant metagenome-assembled genomes (MAGs) from nine landfill leachate samples collected from eight cities across China, spanning 42 phyla, 73 classes, 114 orders, 189 families, and 267 genera. Totally, 74.1% of 1168 MAGs could not be classified to any known species and 5.9% of these MAGs belonged to microbial dark matter phyla. Two putative novel classes were discovered from landfill leachate samples. The identification of thousands of novel carbohydrate-active enzymes showed similar richness level compared to the cow rumen microbiota. The methylotrophic methanogenic pathway was speculated to contribute significantly to methane production in the landfill leachate because of its co-occurrence with the acetoclastic and hydrogenotrophic methanogenic pathways. The genetic potential of dissimilatory nitrate reduction to ammonium (DNRA) was observed, implying DNRA may play a role in ammonium generation in landfill leachate. These findings implied that landfill leachate might be a valuable microbial resource repository and filled the previous understanding gaps for both methanogenesis and nitrogen cycling in landfill leachate microbiota. Our study provides a comprehensive genomic catalog and substantially provides unprecedented taxonomic and functional profiles of the landfill leachate microbiota.
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Affiliation(s)
- Chunfang Deng
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing 100871, China
| | - Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Zhiguang Qiu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong 999077, China
| | - Feng Guo
- School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Rong Mu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yang Wu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Xuejiao Qiao
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Liyu Zhang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jay J Cheng
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; Biological & Agricultural Engineering Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing 100871, China
| | - Ke Yu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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42
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Solchaga JI, Busalmen JP, Nercessian D. Unraveling Anaerobic Metabolisms in a Hypersaline Sediment. Front Microbiol 2022; 13:811432. [PMID: 35369499 PMCID: PMC8966722 DOI: 10.3389/fmicb.2022.811432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The knowledge on the microbial diversity inhabiting hypersaline sediments is still limited. In particular, existing data about anaerobic hypersaline archaea and bacteria are scarce and refer to a limited number of genera. The approach to obtain existing information has been almost exclusively attempting to grow every organism in axenic culture on the selected electron acceptor with a variety of electron donors. Here, a different approach has been used to interrogate the microbial community of submerged hypersaline sediment of Salitral Negro, Argentina, aiming at enriching consortia performing anaerobic respiration of different electron acceptor compounds, in which ecological associations can maximize the possibilities of successful growth. Growth of consortia was demonstrated on all offered electron acceptors, including fumarate, nitrate, sulfate, thiosulfate, dimethyl sulfoxide, and a polarized electrode. Halorubrum and Haloarcula representatives are here shown for the first time growing on lactate, using fumarate or a polarized electrode as the electron acceptor; in addition, they are shown also growing in sulfate-reducing consortia. Halorubrum representatives are for the first time shown to be growing in nitrate-reducing consortia, probably thanks to reduction of N2O produced by other consortium members. Fumarate respiration is indeed shown for the first time supporting growth of Halanaeroarchaeum and Halorhabdus belonging to the archaea, as well as growth of Halanaerobium, Halanaerobaculum, Sporohalobacter, and Acetohalobium belonging to the bacteria. Finally, evidence is presented suggesting growth of nanohaloarchaea in anaerobic conditions.
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Affiliation(s)
- Juan Ignacio Solchaga
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Mar del Plata, Argentina
| | - Juan Pablo Busalmen
- Laboratorio de Bioelectroquímica, INTEMA - CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Débora Nercessian
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Mar del Plata, Argentina
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43
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Shu WS, Huang LN. Microbial diversity in extreme environments. Nat Rev Microbiol 2022; 20:219-235. [PMID: 34754082 DOI: 10.1038/s41579-021-00648-y] [Citation(s) in RCA: 107] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.
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Affiliation(s)
- Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
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Biessy L, Pearman JK, Waters S, Vandergoes MJ, Wood SA. Metagenomic insights to the functional potential of sediment microbial communities in freshwater lakes. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.79265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Molecular-based techniques offer considerable potential to provide new insights into the impact of anthropogenic stressors on lake ecosystems. Microbial communities are involved in many geochemical cycling processes in lakes and a greater understanding of their functions could assist in guiding more targeted remedial actions. Recent advances in metagenomics now make it possible to determine the functional potential of entire microbial communities. The present study investigated microbial communities and their functional potential in surface sediments collected from three lakes with differing trophic states and characteristics. Surface sediments were analysed for their nutrient and elemental contents and metagenomics and metabarcoding analysis undertaken. The nutrients content of the surface sediments did not show as distinct a gradient as water chemistry monitoring data, likely reflecting effects of other lake characteristics, in particular, depth. Metabarcoding and metagenomics revealed differing bacterial community composition and functional potential amongst lakes. Amongst the differentially abundant metabolic pathways, the most prominent were clusters in the energy and xenobiotics pathways. Differences in the energy metabolism paths of photosynthesis and oxidative phosphorylation were observed. These were most likely related to changes in the community composition and especially the presence of cyanobacteria in two of the three lakes. Xenobiotic pathways, such as those involving polycyclic aromatic hydrocarbons, were highest in the lakes with the greatest agricultural land-use in their catchment. These results highlight how microbial metagenomics can be used to gain insights into the causes of differences in trophic status amongst lakes.
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Sala D, Grossi V, Agogué H, Leboulanger C, Jézéquel D, Sarazin G, Antheaume I, Bernard C, Ader M, Hugoni M. Influence of aphotic haloclines and euxinia on organic biomarkers and microbial communities in a thalassohaline and alkaline volcanic crater lake. GEOBIOLOGY 2022; 20:292-309. [PMID: 34687126 DOI: 10.1111/gbi.12477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 09/29/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Studies on microbial communities, and their associated organic biomarkers, that are found thriving in the aphotic euxinic waters in modern stratified ecosystems are scarce compared to those undertaken in euxinic photic zones. The Dziani Dzaha (Mayotte, Indian Ocean) is a tropical, saline, alkaline crater lake that has recently been presented as a modern analog of Proterozoic Oceans due to its thalassohaline classification (having water of marine origin) and specific biogeochemical characteristics. Continuous intense photosynthetic production and microbial mineralization keep most of the water column permanently aphotic and anoxic preventing the development of a euxinic (sulfidic and anoxic) photic zone despite a high sulfide/sulfate ratio and the presence of permanent or seasonal haloclines. In this study, the molecular composition of the organic matter in Lake Dziani Dzaha was investigated and compared to the microbial diversity evaluated through 16S rRNA gene amplicon sequencing, over two contrasting seasons (rainy vs. dry) that influence water column stratification. Depth profiles of organic biomarker concentrations (chlorophyll-a and lipid biomarkers) and bacterial and archaeal OTU abundances appeared to be strongly dependent on the presence of aphotic haloclines and euxinia. OTU abundances revealed the importance of specific haloalkaliphilic bacterial and archaeal assemblages in phytoplanktonic biomass recycling and the biogeochemical functioning of the lake, suggesting new haloalkaline non-phototrophic anaerobic microbial precursors for some of the lipid biomarkers. Uncultured Firmicutes from the family Syntrophomonadaceae (Clostridiales), and Bacteroidetes from the ML635J-40 aquatic group, emerged as abundant chemotrophic bacterial members in the anoxic or euxinic waters and were probably responsible for the production of short-chain n-alkenes, wax esters, diplopterol, and tetrahymanol. Halocline-dependent euxinia also had a strong impact on the archaeal community which was dominated by Woesearchaeota in the sulfide-free waters. In the euxinic waters, methanogenic Euryarchaeota from the Methanomicrobia, Thermoplasmata, and WSA2 classes dominated and were likely at the origin of common hydrocarbon biomarkers of methanogens (phytane, pentamethyl-eicosenes, and partially hydrogenated squalene).
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Affiliation(s)
- David Sala
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENSL, UJM, LGL-TPE, Villeurbanne, France
| | - Vincent Grossi
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENSL, UJM, LGL-TPE, Villeurbanne, France
| | - Hélène Agogué
- LIENSs, UMR 7266, La Rochelle Université - CNRS, La Rochelle, France
| | | | - Didier Jézéquel
- Université de Paris, Institut de Physique du Globe de Paris, Paris, France
- INRAE & Université Savoie Mont Blanc, UMR CARRTEL, Thonon-les-Bains, France
| | - Gérard Sarazin
- Université de Paris, Institut de Physique du Globe de Paris, Paris, France
| | - Ingrid Antheaume
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENSL, UJM, LGL-TPE, Villeurbanne, France
| | - Cécile Bernard
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM) MNHN-CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Magali Ader
- Université de Paris, Institut de Physique du Globe de Paris, Paris, France
| | - Mylène Hugoni
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
- Univ Lyon, INSA Lyon, CNRS, UMR 5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France
- Institut Universitaire de France, Paris, France
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Ataeian M, Liu Y, Kouris A, Hawley AK, Strous M. Ecological Interactions of Cyanobacteria and Heterotrophs Enhances the Robustness of Cyanobacterial Consortium for Carbon Sequestration. Front Microbiol 2022; 13:780346. [PMID: 35222325 PMCID: PMC8880816 DOI: 10.3389/fmicb.2022.780346] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/19/2022] [Indexed: 12/21/2022] Open
Abstract
Lack of robustness is a major barrier to foster a sustainable cyanobacterial biotechnology. Use of cyanobacterial consortium increases biodiversity, which provides functional redundancy and prevents invading species from disrupting the production ecosystem. Here we characterized a cyanobacterial consortium enriched from microbial mats of alkaline soda lakes in BC, Canada, at high pH and alkalinity. This consortium has been grown in open laboratory culture for 4 years without crashes. Using shotgun metagenomic sequencing, 29 heterotrophic metagenome-assembled-genomes (MAGs) were retrieved and were assigned to Bacteroidota, Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobiota, Patescibacteria, Planctomycetota, and Archaea. In combination with metaproteomics, the overall stability of the consortium was determined under different cultivation conditions. Genome information from each heterotrophic population was investigated for six ecological niches created by cyanobacterial metabolism and one niche for phototrophy. Genome-resolved metaproteomics with stable isotope probing using 13C-bicarbonate (protein/SIP) showed tight coupling of carbon transfer from cyanobacteria to the heterotrophic populations, specially Wenzhouxiangella. The community structure was compared to a previously described consortium of a closely related cyanobacteria, which indicated that the results may be generalized. Productivity losses associated with heterotrophic metabolism were relatively small compared to other losses during photosynthesis.
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Affiliation(s)
- Maryam Ataeian
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Yihua Liu
- Department Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Angela Kouris
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Alyse K. Hawley
- School of Engineering, University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
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Mujakić I, Piwosz K, Koblížek M. Phylum Gemmatimonadota and Its Role in the Environment. Microorganisms 2022; 10:microorganisms10010151. [PMID: 35056600 PMCID: PMC8779627 DOI: 10.3390/microorganisms10010151] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/06/2023] Open
Abstract
Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. Currently, the phylum contains only six cultured species. However, data from culture-independent studies indicate that members of Gemmatimonadota are common in diverse habitats. They are abundant in soils, where they seem to be frequently associated with plants and the rhizosphere. Moreover, Gemmatimonadota were found in aquatic environments, such as freshwaters, wastewater treatment plants, biofilms, and sediments. An important discovery was the identification of purple bacterial reaction centers and anoxygenic photosynthesis in this phylum, genes for which were likely acquired via horizontal gene transfer. So far, the capacity for anoxygenic photosynthesis has been described for two cultured species: Gemmatimonas phototrophica and Gemmatimonas groenlandica. Moreover, analyses of metagenome-assembled genomes indicate that it is also common in uncultured lineages of Gemmatimonadota. This review summarizes the current knowledge about this understudied bacterial phylum with an emphasis on its environmental distribution.
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Affiliation(s)
- Izabela Mujakić
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradská 237, 379 81 Třeboň, Czech Republic; (I.M.); (K.P.)
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
| | - Kasia Piwosz
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradská 237, 379 81 Třeboň, Czech Republic; (I.M.); (K.P.)
- National Marine Fisheries Research Institute, Kołłątaja 1, 81-332 Gdynia, Poland
| | - Michal Koblížek
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradská 237, 379 81 Třeboň, Czech Republic; (I.M.); (K.P.)
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
- Correspondence:
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Balaji A, Sapoval N, Seto C, Leo Elworth R, Fu Y, Nute MG, Savidge T, Segarra S, Treangen TJ. KOMB: K-core based de novo characterization of copy number variation in microbiomes. Comput Struct Biotechnol J 2022; 20:3208-3222. [PMID: 35832621 PMCID: PMC9249589 DOI: 10.1016/j.csbj.2022.06.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022] Open
Abstract
Characterizing metagenomes via kmer-based, database-dependent taxonomic classification has yielded key insights into underlying microbiome dynamics. However, novel approaches are needed to track community dynamics and genomic flux within metagenomes, particularly in response to perturbations. We describe KOMB, a novel method for tracking genome level dynamics within microbiomes. KOMB utilizes K-core decomposition to identify Structural variations (SVs), specifically, population-level Copy Number Variation (CNV) within microbiomes. K-core decomposition partitions the graph into shells containing nodes of induced degree at least K, yielding reduced computational complexity compared to prior approaches. Through validation on a synthetic community, we show that KOMB recovers and profiles repetitive genomic regions in the sample. KOMB is shown to identify functionally-important regions in Human Microbiome Project datasets, and was used to analyze longitudinal data and identify keystone taxa in Fecal Microbiota Transplantation (FMT) samples. In summary, KOMB represents a novel graph-based, taxonomy-oblivious, and reference-free approach for tracking CNV within microbiomes. KOMB is open source and available for download at https://gitlab.com/treangenlab/komb.
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Affiliation(s)
- Advait Balaji
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Charlie Seto
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - R.A. Leo Elworth
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Yilei Fu
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Michael G. Nute
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Tor Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Santiago Segarra
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
- Corresponding author.
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
- Corresponding author.
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Abstract
Rhodopsins are light-activated proteins displaying an enormous versatility of function as cation/anion pumps or sensing environmental stimuli and are widely distributed across all domains of life. Even with wide sequence divergence and uncertain evolutionary linkages between microbial (type 1) and animal (type 2) rhodopsins, the membrane orientation of the core structural scaffold of both was presumed universal. This was recently amended through the discovery of heliorhodopsins (HeRs; type 3), that, in contrast to known rhodopsins, display an inverted membrane topology and yet retain similarities in sequence, structure, and the light-activated response. While no ion-pumping activity has been demonstrated for HeRs and multiple crystal structures are available, fundamental questions regarding their cellular and ecological function or even their taxonomic distribution remain unresolved. Here, we investigated HeR function and distribution using genomic/metagenomic data with protein domain fusions, contextual genomic information, and gene coexpression analysis with strand-specific metatranscriptomics. We bring to resolution the debated monoderm/diderm occurrence patterns and show that HeRs are restricted to monoderms. Moreover, we provide compelling evidence that HeRs are a novel type of sensory rhodopsins linked to histidine kinases and other two-component system genes across phyla. In addition, we also describe two novel putative signal-transducing domains fused to some HeRs. We posit that HeRs likely function as generalized light-dependent switches involved in the mitigation of light-induced oxidative stress and metabolic circuitry regulation. Their role as sensory rhodopsins is corroborated by their photocycle dynamics and their presence/function in monoderms is likely connected to the higher sensitivity of these organisms to light-induced damage. IMPORTANCE Heliorhodopsins are enigmatic, novel rhodopsins with a membrane orientation that is opposite to all known rhodopsins. However, their cellular and ecological functions are unknown, and even their taxonomic distribution remains a subject of debate. We provide evidence that HeRs are a novel type of sensory rhodopsins linked to histidine kinases and other two-component system genes across phyla boundaries. In support of this, we also identify two novel putative signal transducing domains in HeRs that are fused with them. We also observe linkages of HeRs to genes involved in mitigation of light-induced oxidative stress and increased carbon and nitrogen metabolism. Finally, we synthesize these findings into a framework that connects HeRs with the cellular response to light in monoderms, activating light-induced oxidative stress defenses along with carbon/nitrogen metabolic circuitries. These findings are consistent with the evolutionary, taxonomic, structural, and genomic data available so far.
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Toshchakov SV, Izotova AO, Vinogradova EN, Kachmazov GS, Tuaeva AY, Abaev VT, Evteeva MA, Gunitseva NM, Korzhenkov AA, Elcheninov AG, Patrushev MV, Kublanov IV. Culture-Independent Survey of Thermophilic Microbial Communities of the North Caucasus. BIOLOGY 2021; 10:biology10121352. [PMID: 34943267 PMCID: PMC8698779 DOI: 10.3390/biology10121352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 01/04/2023]
Abstract
Simple Summary The Republic of North Ossetia-Alania, located in the southern part of the North Caucasus, possess a number of hydrothermal habitats, including both subterranean thermal reservoirs and terrestrial hot springs. At the same time, reports on microbiology of numerous geothermal sites are rather scarce for the whole North Caucasus region. In this paper, we report on the first culture-independent metabarcoding study of thermal habitats in the North Caucasus, coupled with a chemical analysis of the elemental composition of water. The results of this work include the conclusions regarding key metabolic characteristics of these habitats as well as detection of few but abundant deep lineages of uncultivated microorganisms which could be regarded as endemic. This study may represent a first step in closing the knowledge gap in extremophilic microbial communities of the North Caucasus. Abstract The Greater Caucasus is a part of seismically active Alpine–Himalayan orogenic belt and has been a center of significant volcanic activity during the Quaternary period. That led to the formation of the number of hydrothermal habitats, including subterranean thermal aquifers and surface hot springs. However, there are only a limited number of scientific works reporting on the microbial communities of these habitats. Moreover, all these reports concern only studies of specific microbial taxa, carried out using classical cultivation approaches. In this work, we present first culture-independent study of hydrotherms in the Republic of North Ossetia-Alania, located in the southern part of the North Caucasus. Using 16S metabarcoding, we analyzed the composition of the microbial communities of two subterranean thermal aquifers and terrestrial hot springs of the Karmadon valley. Analysis of correlations between the chemical composition of water and the representation of key taxa allowed us to identify the key factors determining the formation of microbial communities. In addition, we were able to identify a significant number of highly abundant deep phylogenetic lineages. Our study represents a first glance on the thermophilic microbial communities of the North Caucasus and may serve as a basis for further microbiological studies of the extreme habitats of this region.
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Affiliation(s)
- Stepan V. Toshchakov
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
- Correspondence: ; Tel.: +7-911-481-1809
| | - Anna O. Izotova
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Elizaveta N. Vinogradova
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow 119991, Russia
| | - Gennady S. Kachmazov
- Faculty of Chemistry, Biology and Biotechnology, North Ossetian State University Named after K.L. Khetagurov, Vatutina str., 44-46, Vladikavkaz 362025, Russia; (G.S.K.); (V.T.A.)
| | - Albina Y. Tuaeva
- National Research Center Kurchatov Institute-GOSNIIGENETIKA, 1st Dorozhny Pr., 1, Moscow 117545, Russia;
| | - Vladimir T. Abaev
- Faculty of Chemistry, Biology and Biotechnology, North Ossetian State University Named after K.L. Khetagurov, Vatutina str., 44-46, Vladikavkaz 362025, Russia; (G.S.K.); (V.T.A.)
| | - Martha A. Evteeva
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Natalia M. Gunitseva
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Aleksei A. Korzhenkov
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Alexander G. Elcheninov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 60-let Oktyzbrya Av., 7/2, Moscow 119071, Russia; (A.G.E.); (I.V.K.)
| | - Maxim V. Patrushev
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 60-let Oktyzbrya Av., 7/2, Moscow 119071, Russia; (A.G.E.); (I.V.K.)
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