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Gios E, Verbruggen E, Audet J, Burns R, Butterbach-Bahl K, Espenberg M, Fritz C, Glatzel S, Jurasinski G, Larmola T, Mander Ü, Nielsen C, Rodriguez AF, Scheer C, Zak D, Silvennoinen HM. Unraveling microbial processes involved in carbon and nitrogen cycling and greenhouse gas emissions in rewetted peatlands by molecular biology. BIOGEOCHEMISTRY 2024; 167:609-629. [PMID: 38707517 PMCID: PMC11068585 DOI: 10.1007/s10533-024-01122-6] [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: 05/31/2023] [Accepted: 01/22/2024] [Indexed: 05/07/2024]
Abstract
Restoration of drained peatlands through rewetting has recently emerged as a prevailing strategy to mitigate excessive greenhouse gas emissions and re-establish the vital carbon sequestration capacity of peatlands. Rewetting can help to restore vegetation communities and biodiversity, while still allowing for extensive agricultural management such as paludiculture. Belowground processes governing carbon fluxes and greenhouse gas dynamics are mediated by a complex network of microbial communities and processes. Our understanding of this complexity and its multi-factorial controls in rewetted peatlands is limited. Here, we summarize the research regarding the role of soil microbial communities and functions in driving carbon and nutrient cycling in rewetted peatlands including the use of molecular biology techniques in understanding biogeochemical processes linked to greenhouse gas fluxes. We emphasize that rapidly advancing molecular biology approaches, such as high-throughput sequencing, are powerful tools helping to elucidate the dynamics of key biogeochemical processes when combined with isotope tracing and greenhouse gas measuring techniques. Insights gained from the gathered studies can help inform efficient monitoring practices for rewetted peatlands and the development of climate-smart restoration and management strategies. Supplementary Information The online version contains supplementary material available at 10.1007/s10533-024-01122-6.
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Affiliation(s)
- Emilie Gios
- NINA, Norwegian Institute for Nature Research, PO Box 5685, Torgarden, NO-7485 Trondheim, Norway
| | - Erik Verbruggen
- Plants and Ecosystems Research Group, Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk, 2610 Antwerp, Belgium
| | - Joachim Audet
- Department of Ecoscience, Aarhus University, C.F. Møllers Allé, 8000 Aarhus, Denmark
| | - Rachel Burns
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Klaus Butterbach-Bahl
- Institute of Meteorology and Climate Research, Atmospheric Environmental Research, Karlsruhe Institute of Technology, 82467 Garmisch-Partenkirchen, Germany
- Department of Agroecology, Pioneer Center for Research in Sustainable Agricultural Futures (Land-CRAFT), Aarhus University, 8000 Aarhus, Denmark
| | - Mikk Espenberg
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 St., Vanemuise, 51003 Tartu, Estonia
| | - Christian Fritz
- Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Stephan Glatzel
- Department of Geography and Regional Research, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Gerald Jurasinski
- Faculty of Agriculture and Environment, Landscape Ecology and Site Evaluation, University of Rostock, Justus-von-Liebig-Weg 6, 18059 Rostock, Germany
- Department of Maritime Systems, Faculty of Interdisciplinary Research, University of Rostock, Albert- Einstein-Straße 3, 18059 Rostock, Germany
| | - Tuula Larmola
- Natural Resources Institute Finland (Luke), 00790 Helsinki, Finland
| | - Ülo Mander
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 St., Vanemuise, 51003 Tartu, Estonia
| | - Claudia Nielsen
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Blichers Alle 20, 8830 Tjele, Denmark
- CBIO, Centre for Circular Bioeconomy, Aarhus University, 8830 Tjele, Denmark
| | - Andres F. Rodriguez
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Blichers Alle 20, 8830 Tjele, Denmark
| | - Clemens Scheer
- Institute of Meteorology and Climate Research, Atmospheric Environmental Research, Karlsruhe Institute of Technology, 82467 Garmisch-Partenkirchen, Germany
| | - Dominik Zak
- Department of Ecoscience, Aarhus University, C.F. Møllers Allé, 8000 Aarhus, Denmark
- Department of Ecohydrology and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, Germany
| | - Hanna M. Silvennoinen
- NINA, Norwegian Institute for Nature Research, PO Box 5685, Torgarden, NO-7485 Trondheim, Norway
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Sabrekov AF, Semenov MV, Terentieva IE, Krasnov GS, Kharitonov SL, Glagolev MV, Litti YV. Anaerobic methane oxidation is quantitatively important in deeper peat layers of boreal peatlands: Evidence from anaerobic incubations, in situ stable isotopes depth profiles, and microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170213. [PMID: 38278226 DOI: 10.1016/j.scitotenv.2024.170213] [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: 09/28/2023] [Revised: 01/07/2024] [Accepted: 01/14/2024] [Indexed: 01/28/2024]
Abstract
Boreal peatlands store most of their carbon in layers deeper than 0.5 m under anaerobic conditions, where carbon dioxide and methane are produced as terminal products of organic matter degradation. Since the global warming potential of methane is much greater than that of carbon dioxide, the balance between the production rates of these gases is important for future climate predictions. Herein, we aimed to understand whether anaerobic methane oxidation (AMO) could explain the high CO2/CH4 anaerobic production ratios that are widely observed for the deeper peat layers of boreal peatlands. Furthermore, we quantified the metabolic pathways of methanogenesis to examine whether hydrogenotrophic methanogenesis is a dominant methane production pathway for the presumably recalcitrant deeper peat. To assess the CH4 cycling in deeper peat, we combined laboratory anaerobic incubations with a pathway-specific inhibitor, in situ depth patterns of stable isotopes in CH4, and 16S rRNA gene amplicon sequencing for three representative boreal peatlands in Western Siberia. We found up to a 69 % reduction in CH4 production due to AMO, which largely explained the high CO2/CH4 anaerobic production ratios and the in situ depth-related patterns of δ13C and δD in methane. The absence of acetate accumulation after inhibiting acetotrophic methanogenesis and the presence of sulfate- and nitrate-reducing anaerobic acetate oxidizers in the deeper peat indicated that these microorganisms use SO42- and NO3- as electron acceptors. Acetotrophic methanogenesis dominated net CH4 production in the deeper peat, accounting for 81 ± 13 %. Overall, anaerobic oxidation is quantitatively important for the methane cycle in the deeper layers of boreal peatlands, affecting both methane and its main precursor concentrations.
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Affiliation(s)
- Aleksandr F Sabrekov
- UNESCO Department "Environmental Dynamics and Global Climate Changes", Ugra State University, Khanty-Mansiysk, Russia.
| | - Mikhail V Semenov
- Laboratory of Soil Carbon and Microbial Ecology, Dokuchaev Soil Science Institute, Moscow, Russia
| | | | - George S Krasnov
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Mikhail V Glagolev
- UNESCO Department "Environmental Dynamics and Global Climate Changes", Ugra State University, Khanty-Mansiysk, Russia; Faculty of Soil Science, Lomonosov Moscow State University, Moscow, Russia
| | - Yuriy V Litti
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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Wang M, Sun M, Zhao Y, Shi Y, Sun S, Wang S, Zhou Y, Chen L. Seasonal changes of soil microbiota and its association with environmental factors in coal mining subsidence area. AMB Express 2023; 13:147. [PMID: 38123764 PMCID: PMC10733236 DOI: 10.1186/s13568-023-01653-5] [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: 10/08/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND As a special type of wetland, the new wetland in the coal mining subsidence area is highly sensitive to environmental changes. In recent years, more and more attention has been paid to the studies of soil microbial diversity in newly born wetlands in coal mining subsidence areas. However, there are few reports on the seasonal variation of soil microbial diversity and its relationship with soil physical and chemical properties. METHODS In this study, 16S rRNA gene sequencing technology was used to analyze the seasonal changes of soil microbial composition and functional diversity in newly formed wetlands in coal mining subsidence areas, and to determine the seasonal changes of soil nutrient elements and physical and chemical properties in coal mining subsidence areas, so as to analyze the correlation between soil microbial diversity and soil nutrient elements and physical and chemical properties in newly formed wetlands in coal mining subsidence areas. RESULTS A total of 16,050 OTUs were obtained after sample gene noise reduction. Proteobacteria, Acidobacteriota and Bacteroidota were the highest abundance in the coal mining subsidence area of Jining. The two seasons gathered separately, and temperature (Temp), total phosphorus (TP), available phosphorus (AP), total organic carbon (TOC) and dry matter content (DMC) were the key factors for the seasonal change of soil microbial community in the wetland of the coal mining subsidence area of Jining. The contents of Temp, AP and TP were significantly correlated with the abundance of soil microorganisms in summer subsidence area, while the contents of DMC and TOC were significantly correlated with the abundance of soil microorganisms in winter subsidence area. CONCLUSION Soil microbial diversity in coal mining subsidence area was correlated with the seasons. Temp, TP, AP, TOC and DMC were the key factors for the seasonal change of soil microbial community in the wetland of the coal mining subsidence area of Jining.
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Affiliation(s)
- Meng Wang
- Technology Innovation Center of Restoration and Reclamation in Mining induced Subsidence Land, Shandong Provincial Lunan Geology and Exploration Institute (Shandong Provincial Bureau of Geology and Mineral Resources, Ministry of Natural Resources of China, No.2 Geological Brigade), Jining, 272000, China
| | - Mengyao Sun
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Yue Zhao
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Yuying Shi
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Shuo Sun
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Shen Wang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Yiping Zhou
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Lei Chen
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China.
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Seward J, Bräuer S, Beckett P, Roy-Léveillée P, Emilson E, Watmough S, Basiliko N. Recovery of Smelter-Impacted Peat and Sphagnum Moss: a Microbial Perspective. MICROBIAL ECOLOGY 2023; 86:2894-2903. [PMID: 37632540 DOI: 10.1007/s00248-023-02289-5] [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: 05/17/2023] [Accepted: 08/15/2023] [Indexed: 08/28/2023]
Abstract
Peatlands store approximately one-half of terrestrial soil carbon and one-tenth of non-glacial freshwater. Some of these important ecosystems are located near heavy metal emitting smelters. To improve the understanding of smelter impacts and potential recovery after initial pollution controls in the 1970s (roughly 50 years of potential recovery), we sampled peatlands along a distance gradient of 134 km from a smelter in Sudbury, Ontario, Canada, an area with over a century of nickel (Ni) and copper (Cu) mining activity. This work is aimed at evaluating potential shifts in bacterial and archaeal community structures in Sphagnum moss and its underlying peat within smelter-impacted poor fens. In peat, total Ni and Cu concentrations were higher (0.062-0.067 and 0.110-0.208 mg/g, respectively) at sites close to the smelter and exponentially dropped with distance from the smelter. This exponential decrease in Ni concentrations was also observed in Sphagnum. 16S rDNA amplicon sequencing showed that peat and Sphagnum moss host distinct microbiomes with peat accommodating a more diverse community structure. The microbiomes of Sphagnum were dominated by Proteobacteria (62.5%), followed by Acidobacteria (11.9%), with no observable trends with distance from the smelter. Dominance of Acidobacteria (32.4%) and Proteobacteria (29.6%) in peat was reported across all sites. No drift in taxonomy was seen across the distance gradient or from the reference sites, suggesting a potential microbiome recovery toward that of the reference peatlands microbiomes after decades of pollution controls. These results advance the understanding of peat and Sphagnum moss microbiomes, as well as depict the sensitivities and the resilience of peatland ecosystems.
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Affiliation(s)
- James Seward
- Vale Living with Lakes Centre and the School of Natural Sciences, Laurentian University, 935 Ramsey Lake Rd, Sudbury, ON, P3E 2C6, Canada.
| | - Suzanna Bräuer
- Department of Biology, Appalachian State University, 572 Rivers Street, Boone, NC, 28608, USA
| | - Peter Beckett
- Vale Living with Lakes Centre and the School of Natural Sciences, Laurentian University, 935 Ramsey Lake Rd, Sudbury, ON, P3E 2C6, Canada
| | - Pascale Roy-Léveillée
- Department of Geography, Université Laval, Pavillon Abitibi-Price, Quebec, G1V 0A6, Canada
| | - Erik Emilson
- Natural Resources Canada, Great Lakes Forestry Centre, 1219 Queen St. East, Sault Ste. Marie, ON, P6A 2E5, Canada
| | - Shaun Watmough
- School of the Environment, Trent University, Peterborough, Ontario, Canada
| | - Nathan Basiliko
- Department of Natural Resources Management, Lakehead University, 955 Oliver Rd., Thunder Bay, ON, P7B 5E1, Canada
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Dedysh SN. Describing difficult-to-culture bacteria: Taking a shortcut or investing time to discover something new? Syst Appl Microbiol 2023; 46:126439. [PMID: 37413783 DOI: 10.1016/j.syapm.2023.126439] [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: 02/27/2023] [Revised: 06/17/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
Despite the growing interest in isolating representatives of poorly studied and as-yet-uncultivated bacterial phylogenetic groups, these microorganisms remain difficult objects for taxonomic studies. The time required for describing one of these fastidious bacteria is commonly measured in several years. What is even more problematic, many routine laboratory tests, which were originally developed for fast-growing and fast-responding microorganisms, are not fully suitable for many environmentally relevant, slow-growing bacteria. Standard techniques used in chemotaxonomic analyses do not identify unique lipids produced by these bacteria. A common practice of preparing taxonomic descriptions that report a minimal set of features to name a newly isolated organism deepens a gap between microbial ecologists and taxonomists. By contrast, investing time in detailed analysis of cell biology and experimental verification of genome-encoded capabilities of newly isolated microorganisms opens a window for novel, unexpected findings, which may shape our ideas about the functional role of these microbes in the environment.
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Affiliation(s)
- Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
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Bandla A, Mukhopadhyay S, Mishra S, Sudarshan AS, Swarup S. Genome-resolved carbon processing potential of tropical peat microbiomes from an oil palm plantation. Sci Data 2023; 10:373. [PMID: 37291271 PMCID: PMC10250450 DOI: 10.1038/s41597-023-02267-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
Tropical peatlands in South-East Asia are some of the most carbon-dense ecosystems in the world. Extensive repurposing of such peatlands for forestry and agriculture has resulted in substantial microbially-driven carbon emissions. However, we lack an understanding of the microorganisms and their metabolic pathways involved in carbon turnover. Here, we address this gap by reconstructing 764 sub-species-level genomes from peat microbiomes sampled from an oil palm plantation located on a peatland in Indonesia. The 764 genomes cluster into 333 microbial species (245 bacterial and 88 archaeal), of which, 47 are near-complete (completeness ≥90%, redundancy ≤5%, number of unique tRNAs ≥18) and 170 are substantially complete (completeness ≥70%, redundancy ≤10%). The capacity to respire amino acids, fatty acids, and polysaccharides was widespread in both bacterial and archaeal genomes. In contrast, the ability to sequester carbon was detected only in a few bacterial genomes. We expect our collection of reference genomes to help fill some of the existing knowledge gaps about microbial diversity and carbon metabolism in tropical peatlands.
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Affiliation(s)
- Aditya Bandla
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore.
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore.
| | - Sourav Mukhopadhyay
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Shailendra Mishra
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
| | | | - Sanjay Swarup
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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7
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Dziurzynski M, Gorecki A, Pawlowska J, Istel L, Decewicz P, Golec P, Styczynski M, Poszytek K, Rokowska A, Gorniak D, Dziewit L. Revealing the diversity of bacteria and fungi in the active layer of permafrost at Spitsbergen island (Arctic) - Combining classical microbiology and metabarcoding for ecological and bioprospecting exploration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159072. [PMID: 36179845 DOI: 10.1016/j.scitotenv.2022.159072] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Arctic soils are constantly subjected to extreme environmental conditions such as low humidity, strong winds, high salinity, freeze-thaw cycles, UV exposition, and low nutrient availability, therefore, they have developed unique microbial ecosystems. These environments provide excellent opportunities to study microbial ecology and evolution within pristine (i.e. with limited anthropogenic influence) regions since the High Arctic is still considered one of the wildest and least explored environments on the planet. This environment is also of interest for the screening and recovery of unique microbial strains suitable for various biotechnological applications. In this study, a combination of culture-depended and culture-independent approaches was used to determine the cultivation bias in studies of the diversity of cold-active microorganisms. Cultivation bias is a reduction in recovered diversity, introduced when applying a classical culturing technique. Six different soil types, collected in the vicinity of the Polish Polar Station Hornsund (Spitsbergen, Norway), were tested. It was revealed that the used media allowed recovery of only 6.37 % of bacterial and 20 % of fungal genera when compared with a culture-independent approach. Moreover, it was shown that a combination of R2A and Marine Broth media recovered as much as 93.6 % of all cultivable bacterial genera detected in this study. Based on these results, a novel protocol for genome-guided bioprospecting, combining a culture-dependent approach, metabarcoding, next-generation sequencing, and genomic data reuse was developed. With this methodology, 14 psychrotolerant, multi-metal-resistant strains, including the highly promising Rhodococcus spp., were obtained. These strains, besides increased metal tolerance, have a petroleum hydrocarbon utilization capacity, and thus may be good candidates for future bioremediation technologies, also suited to permanently cold regions.
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Affiliation(s)
- Mikolaj Dziurzynski
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Adrian Gorecki
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Julia Pawlowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-89 Warsaw, Poland
| | - Lukasz Istel
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-89 Warsaw, Poland
| | - Przemyslaw Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Piotr Golec
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Michal Styczynski
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Krzysztof Poszytek
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Anna Rokowska
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Dorota Gorniak
- Department of Microbiology and Mycology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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Dedysh SN, Ivanova AA, Begmatov SA, Beletsky AV, Rakitin AL, Mardanov AV, Philippov DA, Ravin NV. Acidobacteria in Fens: Phylogenetic Diversity and Genome Analysis of the Key Representatives. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722601440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Building a Cell House from Cellulose: The Case of the Soil Acidobacterium Acidisarcina polymorpha SBC82T. Microorganisms 2022; 10:microorganisms10112253. [DOI: 10.3390/microorganisms10112253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/11/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Acidisarcina polymorpha SBC82T is a recently described representative of the phylum Acidobacteriota from lichen-covered tundra soil. Cells of this bacterium occur within unusual saccular chambers, with the chamber envelope formed by tightly packed fibrils. These extracellular structures were most pronounced in old cultures of strain SBC82T and were organized in cluster-like aggregates. The latter were efficiently destroyed by incubating cell suspensions with cellulase, thus suggesting that they were composed of cellulose. The diffraction pattern obtained for 45-day-old cultures of strain SBC82T by using small angle X-ray scattering was similar to those reported earlier for mature wood samples. The genome analysis revealed the presence of a cellulose biosynthesis locus bcs. Cellulose synthase key subunits A and B were encoded by the bcsAB gene whose close homologs are found in genomes of many members of the order Acidobacteriales. More distant homologs of the acidobacterial bcsAB occurred in representatives of the Proteobacteria. A unique feature of bcs locus in strain SBC82T was the non-orthologous displacement of the bcsZ gene, which encodes the GH8 family glycosidase with a GH5 family gene. Presumably, these cellulose-made extracellular structures produced by A. polymorpha have a protective function and ensure the survival of this acidobacterium in habitats with harsh environmental conditions.
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Wang H, Yun H, Ma X, Li M, Qi M, Wang L, Li Z, Gao S, Tao Y, Liang B, Wang A. Bioelectrochemical catabolism of triclocarban through the cascade acclimation of triclocarban-hydrolyzing and chloroanilines-oxidizing microbial communities. ENVIRONMENTAL RESEARCH 2022; 210:112880. [PMID: 35123970 DOI: 10.1016/j.envres.2022.112880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Chlorinated antimicrobial triclocarban (3,4,4'-trichlorocarbanilide, TCC) is an emerging refractory contaminant omnipresent in various environments. Preferential microbial hydrolysis of TCC to chloroanilines is essential for its efficient mineralization. However, the microbial mineralization of TCC in domestic wastewater is poorly understood. Here, the bioelectrochemical catabolism of TCC to chloroanilines (3,4-dichloroaniline and 4-chloroaniline) and then to CO2 was realized through the cascade acclimation of TCC-hydrolyzing and chloroanilines-oxidizing microbial communities. The biodegradation of chloroanilines was obviously enhanced in the bioelectrochemical reactors. Pseudomonas, Diaphorobacter, and Sphingomonas were the enriched TCC or chloroanilines degraders in the bioelectrochemical reactors. The addition of TCC enhanced the synergistic effect within functional microbial communities based on the feature of the phylogenetic ecological networks. This study provides a new idea for the targeted domestication and construction of functionally differentiated microbial communities to efficiently remove TCC from domestic wastewater through a green and low-carbon bioelectrochemical method.
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Affiliation(s)
- Hao Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Hui Yun
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiaodan Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Minghan Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Mengyuan Qi
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Ling Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Zhiling Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Shuhong Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China; State Key Laboratory of Urban Water Resource and Environment, Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China
| | - Yu Tao
- State Key Laboratory of Urban Water Resource and Environment, Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China; State Key Laboratory of Urban Water Resource and Environment, Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China.
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China; State Key Laboratory of Urban Water Resource and Environment, Shenzhen Key Laboratory of Organic Pollution Prevention and Control, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China
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11
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Paracidobacterium acidisoli gen. nov., sp. nov. and Alloacidobacterium dinghuense gen. nov., sp. nov., two acidobacteria isolated from forest soil, and reclassification of Acidobacterium ailaaui and Acidipila dinghuensis as Pseudacidobacterium ailaaui gen. nov., comb. nov. and Silvibacterium dinghuense comb. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005415] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two aerobic and obligately acidophilic bacteria, designated 4G-K13T and 4Y35T, were isolated from the forest soil sampled at Dinghushan Biosphere Reserve, Guangdong Province, PR China. These two strains were Gram-stain-negative, non-motile and short rods that multiplied by binary division. Strains 4G-K13T and 4Y35T had the highest 16S rRNA gene sequence similarity of 97.0 and 97.2 % to
Silvibacterium bohemicum
DSM 103733T and
Acidisarcina polymorpha
SBC82T, respectively. Phylogenetic trees based on the 16S rRNA gene and whole genome sequences showed consistently that these two strains formed a major clade with members of the genera
Acidipila
,
Acidisarcina
,
Silvibacterium
and
Acidobacterium
in the family
Acidobacteriaceae
, but each occupied an unique position. In both the UBCG and the PhyloPhlAn phylogenomic trees, strains 4G-K13T and 4Y35T congruently formed a highly supported subclade with
Acidobacterium capsulatum
DSM 11244T and
Acidobacterium ailaaui
DSM 27394T, respectively. The major fatty acids (>5 %) of strain 4G-K13T were iso-C15 : 0, iso-C17 : 0, summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) and summed feature 9 (iso-C17 : 1
ω9c and/or C16 : 0 10-methyl), while that of strain 4Y35T were C16 : 0, C18 : 1
ω9c, iso-C15 : 0, summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) and summed feature 9 (iso-C17 : 1
ω9c and/or C16 : 0 10-methyl). Strain 4G-K13T contained phosphatidylethanolamine, four unidentified phospholipids, four glycolipids, two unidentified aminolipids and two unknown lipids, while strain 4Y35T had phosphatidylethanolamine, three unidentified phospholipids, two glycolipids, five unidentified aminolipids and one unknown polar lipid. The DNA G+C contents of 4G-K13T and 4Y35T were 60.5 and 55.8 mol%, respectively. Based on all these phylogenetic, physiological and chemotaxonomic data, we suggest that strains 4G-K13T and 4Y35T represent two novel species of two novel genera in the family
Acidobacteriaceae
, for which the names Paracidobacterium acidisoli gen. nov., sp. nov. (type strain: 4G-K13T=GDMCC 1.1195T=NBRC 113249T) and Alloacidobacterium dinghuense gen. nov., sp. nov. (type strain: 4Y35T=KACC 21728T=NBRC 114261T) are proposed. We also propose to reclassify
Acidobacterium ailaaui
and
Acidipila dinghuensis
as Pseudacidobacterium ailaaui gen. nov., comb. nov. and Silvibacterium dinghuense comb. nov., respectively, based mainly on the results of phylogenomic analysis.
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12
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Huber KJ, Vieira S, Sikorski J, Wüst PK, Fösel BU, Gröngröft A, Overmann J. Differential Response of Acidobacteria to Water Content, Soil Type, and Land Use During an Extended Drought in African Savannah Soils. Front Microbiol 2022; 13:750456. [PMID: 35222321 PMCID: PMC8874233 DOI: 10.3389/fmicb.2022.750456] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Although climate change is expected to increase the extent of drylands worldwide, the effect of drought on the soil microbiome is still insufficiently understood as for dominant but little characterized phyla like the Acidobacteria. In the present study the active acidobacterial communities of Namibian soils differing in type, physicochemical parameters, and land use were characterized by high-throughput sequencing. Water content, pH, major ions and nutrients were distinct for sandy soils, woodlands or dry agriculture on loamy sands. Soils were repeatedly sampled over a 2-year time period and covered consecutively a strong rainy, a dry, a normal rainy and a weak rainy season. The increasing drought had differential effects on different soils. Linear modeling of the soil water content across all sampling locations and sampling dates revealed that the accumulated precipitation of the preceding season had only a weak, but statistically significant effect, whereas woodland and irrigation exerted a strong positive effect on water content. The decrease in soil water content was accompanied by a pronounced decrease in the fraction of active Acidobacteria (7.9-0.7%) while overall bacterial community size/cell counts remained constant. Notably, the strongest decline in the relative fraction of Acidobacteria was observed after the first cycle of rainy and dry season, rather than after the weakest rainy season at the end of the observation period. Over the 2-year period, also the β-diversity of soil Acidobacteria changed. During the first year this change in composition was related to soil type (loamy sand) and land use (woodland) as explanatory variables. A total of 188 different acidobacterial sequence variants affiliated with the "Acidobacteriia," Blastocatellia, and Vicinamibacteria changed significantly in abundance, suggesting either drought sensitivity or formation of dormant cell forms. Comparative physiological testing of 15 Namibian isolates revealed species-specific and differential responses in viability during long-term continuous desiccation or drying-rewetting cycles. These different responses were not determined by phylogenetic affiliation and provide a first explanation for the effect of drought on soil Acidobacteria. In conclusion, the response of acidobacterial communities to water availability is non-linear, most likely caused by the different physiological adaptations of the different taxa present.
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Affiliation(s)
- Katharina J. Huber
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Selma Vieira
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Johannes Sikorski
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Pia K. Wüst
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Bärbel U. Fösel
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alexander Gröngröft
- Department of Geosciences, Institute of Soil Science, University of Hamburg, Hamburg, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
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13
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Sikorski J, Baumgartner V, Birkhofer K, Boeddinghaus RS, Bunk B, Fischer M, Fösel BU, Friedrich MW, Göker M, Hölzel N, Huang S, Huber KJ, Kandeler E, Klaus VH, Kleinebecker T, Marhan S, von Mering C, Oelmann Y, Prati D, Regan KM, Richter-Heitmann T, Rodrigues JFM, Schmitt B, Schöning I, Schrumpf M, Schurig E, Solly EF, Wolters V, Overmann J. The Evolution of Ecological Diversity in Acidobacteria. Front Microbiol 2022; 13:715637. [PMID: 35185839 PMCID: PMC8847707 DOI: 10.3389/fmicb.2022.715637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
Acidobacteria occur in a large variety of ecosystems worldwide and are particularly abundant and highly diverse in soils. In spite of their diversity, only few species have been characterized to date which makes Acidobacteria one of the most poorly understood phyla among the domain Bacteria. We used a culture-independent niche modeling approach to elucidate ecological adaptations and their evolution for 4,154 operational taxonomic units (OTUs) of Acidobacteria across 150 different, comprehensively characterized grassland soils in Germany. Using the relative abundances of their 16S rRNA gene transcripts, the responses of active OTUs along gradients of 41 environmental variables were modeled using hierarchical logistic regression (HOF), which allowed to determine values for optimum activity for each variable (niche optima). By linking 16S rRNA transcripts to the phylogeny of full 16S rRNA gene sequences, we could trace the evolution of the different ecological adaptations during the diversification of Acidobacteria. This approach revealed a pronounced ecological diversification even among acidobacterial sister clades. Although the evolution of habitat adaptation was mainly cladogenic, it was disrupted by recurrent events of convergent evolution that resulted in frequent habitat switching within individual clades. Our findings indicate that the high diversity of soil acidobacterial communities is largely sustained by differential habitat adaptation even at the level of closely related species. A comparison of niche optima of individual OTUs with the phenotypic properties of their cultivated representatives showed that our niche modeling approach (1) correctly predicts those physiological properties that have been determined for cultivated species of Acidobacteria but (2) also provides ample information on ecological adaptations that cannot be inferred from standard taxonomic descriptions of bacterial isolates. These novel information on specific adaptations of not-yet-cultivated Acidobacteria can therefore guide future cultivation trials and likely will increase their cultivation success.
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Affiliation(s)
- Johannes Sikorski
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Vanessa Baumgartner
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Klaus Birkhofer
- Department of Ecology, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Runa S. Boeddinghaus
- Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Boyke Bunk
- Bioinformatics Group, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Fischer
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Bärbel U. Fösel
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael W. Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Markus Göker
- Bioinformatics Group, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Norbert Hölzel
- Biodiversity and Ecosystem Research Group, Institute of Landscape Ecology, University Münster, Münster, Germany
| | - Sixing Huang
- Bioinformatics Group, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Katharina J. Huber
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ellen Kandeler
- Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | | | - Till Kleinebecker
- Institute of Landscape Ecology and Resources Management, University of GieBen, GieBen, Germany
| | - Sven Marhan
- Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | | | - Daniel Prati
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Kathleen M. Regan
- Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - João F. Matias Rodrigues
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Barbara Schmitt
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Ingo Schöning
- Department for Biogeochemical Processes and Biogeochemical Integration, Max-Planck Institute for Biogeochemistry, Jena, Germany
| | - Marion Schrumpf
- Department for Biogeochemical Processes and Biogeochemical Integration, Max-Planck Institute for Biogeochemistry, Jena, Germany
| | | | - Emily F. Solly
- Department for Biogeochemical Processes and Biogeochemical Integration, Max-Planck Institute for Biogeochemistry, Jena, Germany
| | | | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Microbiology, Faculty of Life Sciences, Technische Universität Braunschweig, Braunschweig, Germany
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14
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Wang G, Li Y, Liu J, Chen B, Su H, Liang J, Huang W, Yu K. Comparative Genomics Reveal the Animal-Associated Features of the Acanthopleuribacteraceae Bacteria, and Description of Sulfidibacter corallicola gen. nov., sp., nov. Front Microbiol 2022; 13:778535. [PMID: 35173698 PMCID: PMC8841776 DOI: 10.3389/fmicb.2022.778535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Members of the phylum Acidobacteria are ubiquitous in various environments. Soil acidobacteria have been reported to present a variety of strategies for their success in terrestrial environments. However, owing to lack of pure culture, information on animal-associated acidobacteria are limited, except for those obtained from 16S rRNA genes. To date, only two acidobacteria have been isolated from animals, namely strain M133T obtained from coral Porites lutea and Acanthopleuribacter pedis KCTC 12899T isolated from chiton. Genomics and physiological characteristics of strain M133T and A. pedis KCTC 12899T were compared with 19 other isolates (one strain from each genus) in the phylum Acidobacteria. The results revealed that strain M133T represents a new species in a new genus in the family Acanthopleuribacteraceae. To date, these two Acanthopleuribacteraceae isolates have the largest genomes (10.85–11.79 Mb) in the phylum Acidobacteria. Horizontal gene transfer and gene duplication influenced the structure and plasticity of these large genomes. Dissimilatory nitrate reduction and abundant secondary metabolite biosynthetic gene clusters (including eicosapentaenoic acid de novo biosynthesis) are two distinct features of the Acanthopleuribacteraceae bacteria in the phylum Acidobacteria. The absence of glycoside hydrolases involved in plant polysaccharide degradation and presence of animal disease-related peptidases indicate that these bacteria have evolved to adapt to the animal hosts. In addition to low- and high-affinity respiratory oxygen reductases, enzymes for nitrate to nitrogen, and sulfhydrogenase were also detected in strain M133T, suggesting the capacity and flexibility to grow in aerobic and anaerobic environments. This study highlighted the differences in genome structure, carbohydrate and protein utilization, respiration, and secondary metabolism between animal-associated acidobacteria and other acidobacteria, especially the soil acidobacteria, displaying flexibility and versatility of the animal-associated acidobacteria in environmental adaption.
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Affiliation(s)
- Guanghua Wang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Yuanjin Li
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Jianfeng Liu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Biao Chen
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Hongfei Su
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Wen Huang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
- *Correspondence: Kefu Yu,
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15
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Rakitin AL, Begmatov S, Beletsky AV, Philippov DA, Kadnikov VV, Mardanov AV, Dedysh SN, Ravin NV. Highly Distinct Microbial Communities in Elevated Strings and Submerged Flarks in the Boreal Aapa-Type Mire. Microorganisms 2022; 10:microorganisms10010170. [PMID: 35056619 PMCID: PMC8778904 DOI: 10.3390/microorganisms10010170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 02/04/2023] Open
Abstract
Large areas in the northern hemisphere are covered by extensive wetlands, which represent a complex mosaic of raised bogs, eutrophic fens, and aapa mires all in proximity to each other. Aapa mires differ from other types of wetlands by their concave surface, heavily watered by the central part, as well as by the presence of large-patterned string-flark complexes. In this paper, we characterized microbial diversity patterns in the surface peat layers of the neighboring string and flark structures located within the mire site in the Vologda region of European North Russia, using 16S rRNA gene sequencing. The microbial communities in raised strings were clearly distinct from those in submerged flarks. Strings were dominated by the Alpha- and Gammaproteobacteria. Other abundant groups were the Acidobacteriota, Bacteroidota, Verrucomicrobiota, Actinobacteriota, and Planctomycetota. Archaea accounted for only 0.4% of 16S rRNA gene sequences retrieved from strings. By contrast, they comprised about 22% of all sequences in submerged flarks and mostly belonged to methanogenic lineages. Methanotrophs were nearly absent. Other flark-specific microorganisms included the phyla Chloroflexi, Spirochaetota, Desulfobacterota, Beijerinckiaceae- and Rhodomicrobiaceae-affiliated Alphaproteobacteria, and uncultivated groups env.OPS_17 and vadinHA17 of the Bacteroidota. Such pattern probably reflects local anaerobic conditions in the submerged peat layers in flarks.
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Affiliation(s)
- Andrey L. Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Dmitriy A. Philippov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, 152742 Borok, Russia;
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
- Correspondence: or
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16
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Li Y, Heal K, Wang S, Cao S, Zhou C. Chemodiversity of Soil Dissolved Organic Matter and Its Association With Soil Microbial Communities Along a Chronosequence of Chinese Fir Monoculture Plantations. Front Microbiol 2021; 12:729344. [PMID: 34745032 PMCID: PMC8566896 DOI: 10.3389/fmicb.2021.729344] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022] Open
Abstract
The total dissolved organic matter (DOM) content of soil changes after vegetation transformation, but the diversity of the underlying chemical composition has not been explored in detail. Characterizing the molecular diversity of DOM and its fate enables a better understanding of the soil quality of monoculture forest plantations. This study characterized the chemodiversity of soil DOM, assessed the variation of the soil microbial community composition, and identified specific linkages between DOM molecules and microbial community composition in soil samples from a 100-year chronosequence of Chinese fir monoculture plantations. With increasing plantation age, soil total carbon and dissolved organic carbon first decreased and then increased, while soil nutrients, such as available potassium and phosphorus and total nitrogen, potassium, and phosphorus, increased significantly. Lignin/carboxylic-rich alicyclic molecule (CRAM)-like structures accounted for the largest proportion of DOM, while aliphatic/proteins and carbohydrates showed a decreasing trend along the chronosequence. DOM high in H/C (such as lipids and aliphatic/proteins) degraded preferentially, while low-H/C DOM (such as lignin/CRAM-like structures and tannins) showed recalcitrance during stand development. Soil bacterial richness and diversity increased significantly as stand age increased, while soil fungal diversity tended to increase during early stand development and then decrease. The soil microbial community had a complex connectivity and strong interaction with DOM during stand development. Most bacterial phyla, such as Acidobacteria, Chloroflexi, and Firmicutes, were very significantly and positively correlated with DOM molecules. However, Verrucomicrobia and almost all fungi, such as Basidiomycota and Ascomycota, were significantly negatively correlated with DOM molecules. Overall, the community of soil microorganisms interacted closely with the compositional variability of DOM in the monoculture plantations investigated, both by producing and consuming DOM. This suggests that DOM is not intrinsically recalcitrant but instead persists in soils as a result of simultaneous consumption, transformation, and formation by soil microorganisms with extended stand ages of Chinese fir plantations.
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Affiliation(s)
- Ying Li
- University Engineering Research Center of Sustainable Plantation Management, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China.,Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Kate Heal
- School of GeoSciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Shuzhen Wang
- University Engineering Research Center of Sustainable Plantation Management, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Cao
- University Engineering Research Center of Sustainable Plantation Management, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chuifan Zhou
- University Engineering Research Center of Sustainable Plantation Management, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
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17
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Yao T, Liu L, Tan S, Li H, Liu X, Zeng A, Pan L, Li X, Bai L, Liu K, Xing B. Can the multi-walled carbon nanotubes be used to alleviate the phytotoxicity of herbicides in soils? CHEMOSPHERE 2021; 283:131304. [PMID: 34467944 DOI: 10.1016/j.chemosphere.2021.131304] [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: 04/29/2021] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 06/13/2023]
Abstract
Herbicides are commonly used globally. However, residual herbicides in soils for ages often result in phytotoxicity and serious yield loss to subsequent crops. In this paper, the multi-walled carbon nanotubes (MWCNTs) were utilized to amend the herbicide polluted soil, and the adsorption performance of herbicides to MWCNTs amended soil was studied. Results indicate efficient alleviation of herbicide-induced phytotoxicity to rice and tobacco due to MWCNTs amendment. When 0.4% MWCNTs were applied, the concentration of sulfentrazone that inhibited the same rice height by 50% (IC50) increased to more than 3 times that of pure soil. When the MWCNTs were used to alleviate the phytotoxicity of quinclorac to tobacco, the MWCNTs not only alleviated the phytotoxicity of quinclorac but also promoted the growth of tobacco. The MWCNTs amended soil significantly increased the adsorption of herbicide to soil than biochar. The soil microbial analysis shows that MWCNTs had no significant effect on soil microbial community diversity, but the long-term exposure to MWCNTs could change the structure of the soil microbial community. Above all, our results highlighted the potential implication of the MWCNTs to ensure crop production by promoting crop growth and reducing the residual bioavailability of herbicides.
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Affiliation(s)
- Ting Yao
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China
| | - Lejun Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China
| | - Shuo Tan
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China
| | - Hui Li
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, United States
| | - Xiangying Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China; Hunan Weed Science Key Laboratory, Hunan Academy of Agriculture Science, Changsha, 410125, PR China
| | - Aiping Zeng
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China
| | - Lang Pan
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China
| | - Xiaogang Li
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China
| | - Lianyang Bai
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China; Hunan Weed Science Key Laboratory, Hunan Academy of Agriculture Science, Changsha, 410125, PR China
| | - Kailin Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China; Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, 01003, United States.
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, 01003, United States
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18
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Rodrigues GR, Pinto OHB, Schroeder LF, Fernandes GDR, Costa OYA, Quirino BF, Kuramae EE, Barreto CC. Unraveling the xylanolytic potential of Acidobacteria bacterium AB60 from Cerrado soils. FEMS Microbiol Lett 2021; 367:5902847. [PMID: 32897365 DOI: 10.1093/femsle/fnaa149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/02/2020] [Indexed: 11/13/2022] Open
Abstract
The presence of genes for glycosyl hydrolases in many Acidobacteria genomes indicates an important role in the degradation of plant cell wall material. Acidobacteria bacterium AB60 was obtained from Cerrado oligotrophic soil in Brazil, where this phylum is abundant. The 16S rRNA gene analyses showed that AB60 was closely related to the genera Occallatibacter and Telmatobacter. However, AB60 grew on xylan as carbon source, which was not observed in Occallatibacter species; but growth was not detected on medium containing carboxymethyl cellulose, as observed in Telmatobacter. Nevertheless, the genome analysis of AB60 revealed genes for the enzymes involved in cellulose as well as xylan degradation. In addition to enzymes involved in xylan degradation, α-l-rhamnosidase was detected in the cultures of AB60. Functional screening of a small-insert genomic library did not identify any clones capable of carboxymethyl cellulose degradation, but open reading frames coding α-l-arabinofuranosidase and α-l-rhamnosidase were present in clones showing xylan degradation halos. Both enzymes act on the lateral chains of heteropolymers such as pectin and some hemicelluloses. These results indicate that the hydrolysis of α-linked sugars may offer a metabolic niche for slow-growing Acidobacteria, allowing them to co-exist with other plant-degrading microbes that hydrolyze β-linked sugars from cellulose or hemicellulose backbones.
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Affiliation(s)
- Gisele Regina Rodrigues
- Universidade Católica de Brasília, Graduate Program in Genomic Sciences and Biotechnology, SGAN 916, Brasília, DF 70790-160, Brazil
| | - Otávio Henrique Bezerra Pinto
- Universidade Católica de Brasília, Graduate Program in Genomic Sciences and Biotechnology, SGAN 916, Brasília, DF 70790-160, Brazil
| | - Luís Felipe Schroeder
- Universidade Católica de Brasília, Graduate Program in Genomic Sciences and Biotechnology, SGAN 916, Brasília, DF 70790-160, Brazil
| | | | - Ohana Yonara Assis Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB, Wageningen, The Netherlands
| | - Betania Ferraz Quirino
- Brazilian Agricultural Research Corporation - EMBRAPA/Agroenergy, Brasília, DF 70770-901, Brazil
| | - Eiko Eurya Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB, Wageningen, The Netherlands.,Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CS, Utrecht, The Netherlands
| | - Cristine Chaves Barreto
- Universidade Católica de Brasília, Graduate Program in Genomic Sciences and Biotechnology, SGAN 916, Brasília, DF 70790-160, Brazil
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19
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Recent advances in the bioprospection and applications of chitinolytic bacteria for valorization of waste chitin. Arch Microbiol 2021; 203:1953-1969. [PMID: 33710379 DOI: 10.1007/s00203-021-02234-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 01/12/2021] [Accepted: 02/11/2021] [Indexed: 10/21/2022]
Abstract
One of the most abundant natural polymers on earth, chitin is a fibrous and structural polysaccharide, composed of N-acetyl-D-glucosamine. The biopolymer is the major structural constituent of fungi, arthropods, mollusks, nematodes, and some algae. The biodegradation of chitin is largely manifested by chitinolytic enzyme secreting organisms including bacteria, insects, and plants. Among them, bacterial chitinases represent the most promising, inexpensive, and sustainable source of proteins that can be employed for industrial-scale applications. To this end, the presented review comes at a timely moment to highlight the major sources of chitinolytic bacteria. It also discusses the potential pros and cons of prospecting bacterial chitinases that can be easily manipulated through genetic engineering. Additionally, we have elaborated the recent applications of the chitin thereby branding chitinases as potential candidates for biorefinery and biomedical research for eco-friendly and sustainable management of chitin waste in the environment.
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20
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Rat A, Naranjo HD, Krigas N, Grigoriadou K, Maloupa E, Alonso AV, Schneider C, Papageorgiou VP, Assimopoulou AN, Tsafantakis N, Fokialakis N, Willems A. Endophytic Bacteria From the Roots of the Medicinal Plant Alkanna tinctoria Tausch ( Boraginaceae): Exploration of Plant Growth Promoting Properties and Potential Role in the Production of Plant Secondary Metabolites. Front Microbiol 2021; 12:633488. [PMID: 33633713 PMCID: PMC7901983 DOI: 10.3389/fmicb.2021.633488] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/13/2021] [Indexed: 11/13/2022] Open
Abstract
Alkannin and shikonin (A/S) are enantiomeric naphthoquinones produced in the roots of certain plants from the Boraginaceae family such as Lithospermum spp. and Alkanna spp. They possess antimicrobial, anti-tumoral and wound healing properties. The production of secondary metabolites by Alkanna tinctoria might be influenced by its endomicrobiome. To study the interaction between this medicinal plant and its bacterial endophytes, we isolated bacteria from the roots of wild growing Alkanna tinctoria collected near to Athens and Thessaloniki in Greece. Representative strains selected by MALDI-TOF mass spectrometry were identified by partial 16S rRNA gene sequence analysis. In total, 197 distinct phylotypes of endophytic bacteria were detected. The most abundant genera recovered were Pseudomonas, Xanthomonas, Variovorax, Bacillus, Inquilinus, Pantoea, and Stenotrophomonas. Several bacteria were then tested in vitro for their plant growth promoting activity and the production of cell-wall degrading enzymes. Strains of Pseudomonas, Pantoea, Bacillus and Inquilinus showed positive plant growth properties whereas those of Bacteroidetes and Rhizobiaceae showed pectinase and cellulase activity in vitro. In addition, bacterial responses to alkannin and shikonin were investigated through resistance assays. Gram negative bacteria were found to be resistant to the antimicrobial properties of A/S, whereas the Gram positives were sensitive. A selection of bacteria was then tested for the ability to induce A/S production in hairy roots culture of A. tinctoria. Four strains belonging to Chitinophaga sp., Allorhizobium sp., Duganella sp., and Micromonospora sp., resulted in significantly more A/S in the hairy roots than the uninoculated control. As these bacteria can produce cell-wall degrading enzymes, we hypothesize that the A/S induction may be related with the plant-bacteria interaction during colonization.
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Affiliation(s)
- Angélique Rat
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Faculty Sciences, Ghent University, Ghent, Belgium
| | - Henry D Naranjo
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Faculty Sciences, Ghent University, Ghent, Belgium
| | - Nikos Krigas
- Laboratory of Conservation and Evaluation of Native and Floricultural Species, Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, Thessaloniki, Greece
| | - Katerina Grigoriadou
- Laboratory of Conservation and Evaluation of Native and Floricultural Species, Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, Thessaloniki, Greece
| | - Eleni Maloupa
- Laboratory of Conservation and Evaluation of Native and Floricultural Species, Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, Thessaloniki, Greece
| | | | | | - Vassilios P Papageorgiou
- Organic Chemistry Laboratory, School of Chemical Engineering, Aristotle University of Thessaloniki and Center of Interdisciplinary Research and Innovation of AUTh (CIRI-AUTh), Natural Products Research Centre of Excellence (NatPro-AUTH), Thessaloniki, Greece
| | - Andreana N Assimopoulou
- Organic Chemistry Laboratory, School of Chemical Engineering, Aristotle University of Thessaloniki and Center of Interdisciplinary Research and Innovation of AUTh (CIRI-AUTh), Natural Products Research Centre of Excellence (NatPro-AUTH), Thessaloniki, Greece
| | - Nikolaos Tsafantakis
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikolas Fokialakis
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Anne Willems
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Faculty Sciences, Ghent University, Ghent, Belgium
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21
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Kimeklis AK, Gladkov GV, Zverev AO, Kichko AA, Andronov EE, Ergina EI, Kostenko IV, Abakumov EV. Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula. PeerJ 2021; 9:e10871. [PMID: 33643711 PMCID: PMC7897411 DOI: 10.7717/peerj.10871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/10/2021] [Indexed: 01/04/2023] Open
Abstract
Rendzic Leptosols are intrazonal soils formed on limestone bedrock. The specialty of these soils is that parent rock material is more influential in shaping soil characteristics than zonal factors such as climate, especially during soil formation. Unlike fast evolving Podzols due to their leaching regime, Leptosols do not undergo rapid development due to the nature of the limestone. Little is known how microbiome reflects this process, so we assessed microbiome composition of Rendzic Leptosols of different ages, arising from disruption and subsequent reclamation. The mountains and foothills that cover much of the Crimean Peninsula are ideal for this type of study, as the soils were formed on limestone and have been subjected to anthropogenic impacts through much of human history. Microbiomes of four soil sites forming a chronosequence, including different soil horizons, were studied using sequencing of 16S rRNA gene libraries and quantitative PCR. Dominant phyla for all soil sites were Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Thaumarchaeota, Planctomycetes, Verrucomicrobia and Firmicutes. Alpha diversity was similar across sites and tended to be higher in topsoil. Beta diversity showed that microbiomes diverged according to the soil site and the soil horizon. The oldest and the youngest soils had the most similar microbiomes, which could have been caused by their geographic proximity. Oligotrophic bacteria from Chitinophagaceae, Blastocatellaceae and Rubrobacteriaceae dominated the microbiome of these soils. The microbiome of 700-year old soil was the most diverse. This soil was from the only study location with topsoil formed by plant litter, which provided additional nutrients and could have been the driving force of this differentiation. Consistent with this assumption, this soil was abundant in copiotrophic bacteria from Proteobacteria and Actinobacteria phyla. The microbiome of 50-year old Leptosol was more similar to the microbiome of benchmark soil than the microbiome of 700-year old soil, especially by weighted metrics. CCA analysis, in combination with PERMANOVA, linked differences in microbiomes to the joint change of all soil chemical parameters between soil horizons. Local factors, such as parent material and plant litter, more strongly influenced the microbiome composition in Rendzic Leptosols than soil age.
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Affiliation(s)
- Anastasiia K Kimeklis
- Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia.,Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
| | - Grigory V Gladkov
- Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia.,Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
| | - Aleksei O Zverev
- Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia.,Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
| | - Arina A Kichko
- Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia.,Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
| | - Evgeny E Andronov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia.,Genetics and Biotechnology, St. Petersburg State University, Saint-Petersburg, Russia.,V.V. Dokuchaev Soil Science Institute, Moscow, Russia
| | - Elena I Ergina
- V.I. Vernadsky Crimean Federal University, Simferopol, Russia
| | - Igor V Kostenko
- Nikitsky Botanical Garden -National Scientific Center, Yalta, Russia
| | - Evgeny V Abakumov
- Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia.,Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
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22
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Gonçalves OS, Santana MF. The coexistence of monopartite integrative and conjugative elements in the genomes of Acidobacteria. Gene 2021; 777:145476. [PMID: 33549716 DOI: 10.1016/j.gene.2021.145476] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/15/2021] [Accepted: 01/28/2021] [Indexed: 10/22/2022]
Abstract
Soil bacteria can rapidly adapt to environmental perturbations through horizontal gene transfer. Acidobacteria is one of the most persistent dominant phyla in the soil. However, the role of these organisms in terrestrial ecosystems remains elusive. Here we identified and describe the integrative and conjugative elements (ICEs) in the published complete genomes of Acidobacteria. In total, ten novel ICEs were identified, in which nine were found integrated as three separated monopartite ICEs in the single chromosome sequences of three Acidobacteria. These ICEs carry a repertoire of genes with potential environmental roles, including heavy metal resistance, iron uptake, secondary metabolism, and antibiotic resistance. To our knowledge, these are the first evidence of three monopartite ICEs identified in the single chromosome, and this might be due to the absence of recognizable entry exclusion systems. We hypothesis that the coexistence of multiples ICEs in the chromosome of Acidobacteria might reflect a major advantage for the survival, resistance, and persistence of phylum in the environment.
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Affiliation(s)
- Osiel Silva Gonçalves
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Mateus Ferreira Santana
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil.
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23
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Klarenberg IJ, Keuschnig C, Warshan D, Jónsdóttir IS, Vilhelmsson O. The Total and Active Bacterial Community of the Chlorolichen Cetraria islandica and Its Response to Long-Term Warming in Sub-Arctic Tundra. Front Microbiol 2020; 11:540404. [PMID: 33391192 PMCID: PMC7775390 DOI: 10.3389/fmicb.2020.540404] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 11/30/2020] [Indexed: 01/04/2023] Open
Abstract
Lichens are traditionally defined as a symbiosis between a fungus and a green alga and or a cyanobacterium. This idea has been challenged by the discovery of bacterial communities inhabiting the lichen thalli. These bacteria are thought to contribute to the survival of lichens under extreme and changing environmental conditions. How these changing environmental conditions affect the lichen-associated bacterial community composition remains unclear. We describe the total (rDNA-based) and potentially metabolically active (rRNA-based) bacterial community of the lichen Cetaria islandica and its response to long-term warming using a 20-year warming experiment in an Icelandic sub-Arctic tundra. 16S rRNA and rDNA amplicon sequencing showed that the orders Acetobacterales (of the class Alphaproteobacteria) and Acidobacteriales (of the phylum Acidobacteria) dominated the bacterial community. Numerous amplicon sequence variants (ASVs) could only be detected in the potentially active community but not in the total community. Long-term warming led to increases in relative abundance of bacterial taxa on class, order and ASV level. Warming altered the relative abundance of ASVs of the most common bacterial genera, such as Granulicella and Endobacter. The potentially metabolically active bacterial community was also more responsive to warming than the total community. Our results suggest that the bacterial community of the lichen C. islandica is dominated by acidophilic taxa and harbors disproportionally active rare taxa. We also show for the first time that climate warming can lead to shifts in lichen-associated bacterial community composition.
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Affiliation(s)
- Ingeborg J. Klarenberg
- Natural Resource Sciences, University of Akureyri, Akureyri, Iceland
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Christoph Keuschnig
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS, École Centrale de Lyon, Écully, France
| | - Denis Warshan
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | | | - Oddur Vilhelmsson
- Natural Resource Sciences, University of Akureyri, Akureyri, Iceland
- BioMedical Center, University of Iceland, Reykjavík, Iceland
- School of Biological Sciences, University of Reading, Reading, United Kingdom
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24
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Oberpaul M, Zumkeller CM, Culver T, Spohn M, Mihajlovic S, Leis B, Glaeser SP, Plarre R, McMahon DP, Hammann P, Schäberle TF, Glaeser J, Vilcinskas A. High-Throughput Cultivation for the Selective Isolation of Acidobacteria From Termite Nests. Front Microbiol 2020; 11:597628. [PMID: 33240253 PMCID: PMC7677567 DOI: 10.3389/fmicb.2020.597628] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/19/2020] [Indexed: 12/27/2022] Open
Abstract
Microbial communities in the immediate environment of socialized invertebrates can help to suppress pathogens, in part by synthesizing bioactive natural products. Here we characterized the core microbiomes of three termite species (genus Coptotermes) and their nest material to gain more insight into the diversity of termite-associated bacteria. Sampling a healthy termite colony over time implicated a consolidated and highly stable microbiome, pointing toward the fact that beneficial bacterial phyla play a major role in termite fitness. In contrast, there was a significant shift in the composition of the core microbiome in one nest during a fungal infection, affecting the abundance of well-characterized Streptomyces species (phylum Actinobacteria) as well as less-studied bacterial phyla such as Acidobacteria. High-throughput cultivation in microplates was implemented to isolate and identify these less-studied bacterial phylogenetic group. Amplicon sequencing confirmed that our method maintained the bacterial diversity of the environmental samples, enabling the isolation of novel Acidobacteriaceae and expanding the list of cultivated species to include two strains that may define new species within the genera Terracidiphilus and Acidobacterium.
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Affiliation(s)
- Markus Oberpaul
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Celine M. Zumkeller
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Tanja Culver
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Marius Spohn
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Sanja Mihajlovic
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Benedikt Leis
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Stefanie P. Glaeser
- Institute of Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Rudy Plarre
- Bundesanstalt für Materialforschung und -prüfung, Berlin, Germany
| | - Dino P. McMahon
- Bundesanstalt für Materialforschung und -prüfung, Berlin, Germany
- Institute of Biology, Free University of Berlin, Berlin, Germany
| | - Peter Hammann
- Sanofi-Aventis Deutschland GmbH, R&D Integrated Drug Discovery, Hoechst Industrial Park, Frankfurt am Main, Germany
| | - Till F. Schäberle
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Jens Glaeser
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Andreas Vilcinskas
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
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25
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Kalam S, Basu A, Ahmad I, Sayyed RZ, El-Enshasy HA, Dailin DJ, Suriani NL. Recent Understanding of Soil Acidobacteria and Their Ecological Significance: A Critical Review. Front Microbiol 2020; 11:580024. [PMID: 33193209 PMCID: PMC7661733 DOI: 10.3389/fmicb.2020.580024] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/08/2020] [Indexed: 11/13/2022] Open
Abstract
Acidobacteria represents an underrepresented soil bacterial phylum whose members are pervasive and copiously distributed across nearly all ecosystems. Acidobacterial sequences are abundant in soils and represent a significant fraction of soil microbial community. Being recalcitrant and difficult-to-cultivate under laboratory conditions, holistic, polyphasic approaches are required to study these refractive bacteria extensively. Acidobacteria possesses an inventory of genes involved in diverse metabolic pathways, as evidenced by their pan-genomic profiles. Because of their preponderance and ubiquity in the soil, speculations have been made regarding their dynamic roles in vital ecological processes viz., regulation of biogeochemical cycles, decomposition of biopolymers, exopolysaccharide secretion, and plant growth promotion. These bacteria are expected to have genes that might help in survival and competitive colonization in the rhizosphere, leading to the establishment of beneficial relationships with plants. Exploration of these genetic attributes and more in-depth insights into the belowground mechanics and dynamics would lead to a better understanding of the functions and ecological significance of this enigmatic phylum in the soil-plant environment. This review is an effort to provide a recent update into the diversity of genes in Acidobacteria useful for characterization, understanding ecological roles, and future biotechnological perspectives.
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Affiliation(s)
- Sadaf Kalam
- Department of Biochemistry, St. Ann's College for Women, Hyderabad, India
| | - Anirban Basu
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Iqbal Ahmad
- Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India
| | - R Z Sayyed
- Department of Microbiology, PSGVP Mandal's, Arts, Science and Commerce College, Shahada, India
| | - Hesham Ali El-Enshasy
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,City of Scientific Research and Technological Applications, New Borg El-Arab, Egypt
| | - Daniel Joe Dailin
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia
| | - Ni Luh Suriani
- Biology Department, Faculty of Mathematics and Natural Science, Udayana University, Bali, Indonesia
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26
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Giguere AT, Eichorst SA, Meier DV, Herbold CW, Richter A, Greening C, Woebken D. Acidobacteria are active and abundant members of diverse atmospheric H 2-oxidizing communities detected in temperate soils. ISME JOURNAL 2020; 15:363-376. [PMID: 33024291 PMCID: PMC8027828 DOI: 10.1038/s41396-020-00750-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/30/2020] [Accepted: 08/12/2020] [Indexed: 12/24/2022]
Abstract
Significant rates of atmospheric dihydrogen (H2) consumption have been observed in temperate soils due to the activity of high-affinity enzymes, such as the group 1h [NiFe]-hydrogenase. We designed broadly inclusive primers targeting the large subunit gene (hhyL) of group 1h [NiFe]-hydrogenases for long-read sequencing to explore its taxonomic distribution across soils. This approach revealed a diverse collection of microorganisms harboring hhyL, including previously unknown groups and taxonomically not assignable sequences. Acidobacterial group 1h [NiFe]-hydrogenase genes were abundant and expressed in temperate soils. To support the participation of acidobacteria in H2 consumption, we studied two representative mesophilic soil acidobacteria, which expressed group 1h [NiFe]-hydrogenases and consumed atmospheric H2 during carbon starvation. This is the first time mesophilic acidobacteria, which are abundant in ubiquitous temperate soils, have been shown to oxidize H2 down to below atmospheric concentrations. As this physiology allows bacteria to survive periods of carbon starvation, it could explain the success of soil acidobacteria. With our long-read sequencing approach of group 1h [NiFe]-hydrogenase genes, we show that the ability to oxidize atmospheric levels of H2 is more widely distributed among soil bacteria than previously recognized and could represent a common mechanism enabling bacteria to persist during periods of carbon deprivation.
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Affiliation(s)
- Andrew T Giguere
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Stephanie A Eichorst
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Dimitri V Meier
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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27
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Naumoff DG, Dedysh SN. Chitinases Encoded in the Genomes of Acidobacteria: Origin and Evolution. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720040098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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28
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Varlamov VP, Il'ina AV, Shagdarova BT, Lunkov AP, Mysyakina IS. Chitin/Chitosan and Its Derivatives: Fundamental Problems and Practical Approaches. BIOCHEMISTRY (MOSCOW) 2020; 85:S154-S176. [PMID: 32087058 DOI: 10.1134/s0006297920140084] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this review, we present the data on the natural occurrence of chitin and its partially or fully deacetylated derivative chitosan, as well as their properties, methods of modification, and potential applications of derivatives with bactericidal, fungicidal, and antioxidant activities. The structure and physicochemical characteristics of the polymers, their functions, and features of chitin microbial synthesis and degradation, including the processes occurring in nature, are described. New data on the hydrolytic microorganisms capable of chitin degradation under extreme conditions are presented. Special attention is focused on the effect of physicochemical characteristics of chitosan, including molecular weight, degree of deacetylation, polydispersity index, and number of amino group derivatives (quaternized, succinyl, etc.) on the antimicrobial and antioxidant properties of modified polymers that can be of particular interest for biotechnology, medicine, and agriculture. Analysis of the available literature data confirms the importance of fundamental research to broaden our knowledge on the occurrence of chitin and chitosan in nature, their role in global biosphere cycles, and prospects of applied research aimed at using chitin, chitosan, and their derivatives in various aspects of human activity.
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Affiliation(s)
- V P Varlamov
- Laboratory of Biopolymer Engineering, Institute of Bioengineering, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 117312, Russia.
| | - A V Il'ina
- Laboratory of Biopolymer Engineering, Institute of Bioengineering, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 117312, Russia
| | - B Ts Shagdarova
- Laboratory of Biopolymer Engineering, Institute of Bioengineering, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 117312, Russia
| | - A P Lunkov
- Laboratory of Biopolymer Engineering, Institute of Bioengineering, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 117312, Russia
| | - I S Mysyakina
- Winogradsky Institute of Microbiology, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 117312, Russia
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Ivanova AA, Beletsky AV, Rakitin AL, Kadnikov VV, Philippov DA, Mardanov AV, Ravin NV, Dedysh SN. Closely Located but Totally Distinct: Highly Contrasting Prokaryotic Diversity Patterns in Raised Bogs and Eutrophic Fens. Microorganisms 2020; 8:microorganisms8040484. [PMID: 32235351 PMCID: PMC7232223 DOI: 10.3390/microorganisms8040484] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 01/21/2023] Open
Abstract
Large areas in Northern Russia are covered by extensive mires, which represent a complex mosaic of ombrotrophic raised bogs, minerotrophic and eutrophic fens, all in a close proximity to each other. In this paper, we compared microbial diversity patterns in the surface peat layers of the neighbouring raised bogs and eutrophic fens that are located within two geographically remote mire sites in Vologda region using 16S rRNA gene sequencing. Regardless of location, the microbial communities in raised bogs were highly similar to each other but were clearly distinct from those in eutrophic fens. Bogs were dominated by the Acidobacteria (30%–40% of total 16S rRNA gene reads), which belong to the orders Acidobacteriales and Bryobacterales. Other bog-specific bacteria included the Phycisphaera-like group WD2101 and the families Isosphaeraceae and Gemmataceae of the Planctomycetes, orders Opitutales and Pedosphaerales of the Verrucomicrobia and a particular group of alphaproteobacteria within the Rhizobiales. In contrast, fens hosted Anaerolineae-affiliated Chloroflexi, Vicinamibacteria- and Blastocatellia-affiliated Acidobacteria, Rokubacteria, uncultivated group OM190 of the Planctomycetes and several groups of betaproteobacteria. The Patescibacteria were detected in both types of wetlands but their relative abundance was higher in fens. A number of key parameters that define the distribution of particular bacterial groups in mires were identified.
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Affiliation(s)
- Anastasia A. Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.A.I.); (S.N.D.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.B.); (A.L.R.); (V.V.K.); (A.V.M.)
| | - Andrey L. Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.B.); (A.L.R.); (V.V.K.); (A.V.M.)
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.B.); (A.L.R.); (V.V.K.); (A.V.M.)
| | - Dmitriy A. Philippov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia;
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.B.); (A.L.R.); (V.V.K.); (A.V.M.)
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.B.); (A.L.R.); (V.V.K.); (A.V.M.)
- Correspondence:
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.A.I.); (S.N.D.)
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30
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Linking ecology and systematics of acidobacteria: Distinct habitat preferences of the Acidobacteriia and Blastocatellia in tundra soils. PLoS One 2020; 15:e0230157. [PMID: 32182280 PMCID: PMC7077872 DOI: 10.1371/journal.pone.0230157] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 02/22/2020] [Indexed: 12/26/2022] Open
Abstract
The Acidobacteria is one of the major bacterial phyla in soils and peatlands. The currently explored diversity within this phylum is assigned to 15 class-level units, five of which contain described members. The ecologically relevant traits of acidobacteria from different classes remain poorly understood. Here, we compared the patterns of acidobacterial diversity in sandy soils of tundra, along a gradient of increasing vegetation–unfixed aeolian sand, semi-fixed surfaces with mosses and lichens, and mature soil under fully developed plant cover. The Acidobacteria-affiliated 16S rRNA gene sequences retrieved from these soils comprised 11 to 33% of total bacterial reads and belonged mostly to members of the classes Acidobacteriia and Blastocatellia, which displayed opposite habitat preferences. The relative abundance of the Blastocatellia was maximal in unfixed sands and declined in soils of vegetated plots, showing positive correlation with soil pH and negative correlation with carbon and nitrogen availability. An opposite tendency was characteristic for the Acidobacteriia. Most Blastocatellia-affiliated reads belonged to as-yet-undescribed members of the family Arenimicrobiaceae, which appears to be characteristic for dry, depleted in organic matter soil habitats. The pool of Acidobacteriia-affiliated sequences, apart from Acidobacteriaceae- and Bryobacteraceae-related reads, had a large proportion of sequences from as-yet-undescribed families, which seem to specialize in degrading plant-derived organic matter. This analysis reveals sandy soils of tundra as a source of novel acidobacterial diversity and provides an insight into the ecological preferences of different taxonomic groups within this phylum.
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31
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Li W, Liu X, Niu S. Differential responses of the acidobacterial community in the topsoil and subsoil to fire disturbance in Pinus tabulaeformis stands. PeerJ 2019; 7:e8047. [PMID: 31844567 PMCID: PMC6911345 DOI: 10.7717/peerj.8047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/16/2019] [Indexed: 11/25/2022] Open
Abstract
Acidobacteria is found to be dominant and abundant in forest soil, and performs specific ecological functions (such as cellulose decomposition and photosynthetic capacity, etc.). However, relative limited is known about its changing patterns after a fire interruption. In this study, the response of soil Acidobacteria to a wildfire disturbance was investigated using the Illumina MiSeq sequencing system. The research area was classified by different severities of fire damage (high, moderate, and low severity, and an unburnt area), and samples were collected from various soil layers (0–10 cm as topsoil; 10–20 cm as subsoil). We obtained a total of 986,036 sequence reads; 31.77% of them belonged to Acidobacteria. Overall, 18 different Acidobacteria subgroups were detected, with subgroups 4, 6, 1, 3, and 2 the most abundant, accounting for 31.55%, 30.84%, 17.42%, 6.02%, and 5.81% of acidobacterial sequences across all samples, respectively. Although no significant differences in acidobacterial diversity were found in the same soil layer across different fire severities, we observed significantly lower numbers of reads, but higher Shannon and Simpson indices, in the topsoil of the high-severity fire area than in the subsoil. Non-metric multidimensional scaling (NMDS) analysis and permutational multivariate analysis of variance (PERMANOVA) also revealed significant differences in the acidobacterial community structure between the two soil layers. Soil pH, total nitrogen, NH4+-N, the Shannon index of understory vegetation and canopy density were the major drivers for acidobacterial community structure in the topsoil, while soil pH and organic matter were significant factors in the subsoil. A variance partitioning analysis (VPA) showed that edaphic factors explained the highest variation both in the topsoil (15.6%) and subsoil (56.3%). However, there are large gaps in the understanding of this field of research that still need to be explored in future studies.
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Affiliation(s)
- Weike Li
- Beijing Key Laboratory for Forest Resources and Ecosystem Processes, Beijing Forestry University, Beijing, China.,Fire Engineering, China Fire and Rescue Institute, Beijing, China
| | - Xiaodong Liu
- Beijing Key Laboratory for Forest Resources and Ecosystem Processes, Beijing Forestry University, Beijing, China
| | - Shukui Niu
- Beijing Key Laboratory for Forest Resources and Ecosystem Processes, Beijing Forestry University, Beijing, China
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Lichenibacterium ramalinae gen. nov, sp. nov., Lichenibacterium minor sp. nov., the first endophytic, beta-carotene producing bacterial representatives from lichen thalli and the proposal of the new family Lichenibacteriaceae within the order Rhizobiales. Antonie van Leeuwenhoek 2019; 113:477-489. [PMID: 31741189 DOI: 10.1007/s10482-019-01357-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/06/2019] [Indexed: 12/19/2022]
Abstract
This study of lichens in the subarctic zone of the northern hemisphere has resulted in the detection of new representatives of the order Rhizobiales. The16S rRNA gene sequence phylogeny placed the strains as a separate branch inside the Rhizobiales clade. Strain RmlP001T exhibits 91.85% similarity to Roseiarcus fermentans strain Pf56T and 91.76% to Beijerinckia doebereinerae strain LMG 2819T, whilst strain RmlP026T is closely related to B. doebereinerae strain LMG 2819T (91.85%) and Microvirga pakistanensis strain NCCP-1258T (91.39%). A whole-genome phylogeny of the strains confirmed their taxonomic positions. The cells of both strains were observed to be Gram-negative, motile rods that multiplied by binary fission. The cells were found to contain poly-β-hydroxybutyrate and polyphosphate, to grow at pH 3.5-8.0 and 10-30 °C, and could not fix atmospheric nitrogen. Their major cellular fatty acid identified was C18:1ω7c (68-71%) and their DNA G + C contents determined to be 70.5-70.8%. Beta-carotene was identified as their major carotenoid pigment; Q-10 was the only ubiquinone detected. Strains RmlP001T and RmlP026T are distinguishable from related species by the presence of β-carotene, the absence of C1 metabolism and the ability to grow in the presence of 3.5% NaCl. Based on their phylogenetic, phenotypic and chemotaxonomic features, we propose a novel genus Lichenibacterium and two novel species, Lichenibacterium ramalinae (the type species of the genus) and Lichenibacterium minor, to accommodate these bacteria within the family Lichenibacteriaceae fam. nov. of the order Rhizobiales. The L. ramalinae type strain is RmlP001T (= KCTC 72076T = VKM B-3263T) and the L. minor type strain is RmlP026T (= KCTC 72077T = VKM B-3277T).
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Rakitin A, Beletsky A, Mardanov A, Surgucheva N, Sorokin V, Cherbunina M, Brouchkov A, Mulyukin A, Filippova S. Prokaryotic community in Pleistocene ice wedges of Mammoth Mountain. Extremophiles 2019; 24:93-105. [PMID: 31606813 DOI: 10.1007/s00792-019-01138-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/30/2019] [Indexed: 01/21/2023]
Abstract
Ice wedges differ from other types of surface and underground glacial bodies and are widely spread in perennially frozen sub-Arctic regions, but the bacterial and archaeal diversity in these permafrost features remains poorly studied. Here, we compared the prokaryotic community composition in the active layer and ancient, 13-19 kyr BP and ~ 40 kyr BP, ice wedge horizons from the same exposure profile of the Mammoth Mountain, using pyrosequencing 16S rRNA gene. The most abundant OTUs in the active layer were affiliated with Acidobacteria (31.81%) followed by Actinobacteria (18.29%), Proteobacteria (18.14%), Gemmatimonadetes (7.3%), Parcubacteria (7.13%) and Bacteroidetes (6.49%). The prokaryotic community in 13-19 kyr BP ice wedge differed at the phylum level by the predominance of Actinobacteria (29.15%) over Acidobacteria (19.52%), Proteobacteria (18.45%), Verrumicrobia (5.88%), Firmicutes (2.98%) and Gemmatimonadetes (2.87%). In contrast, the oldest (~ 40 kyr BP) ice wedge prokaryotic community was rather poor, and only three phyla Firmicutes (54.48%), Proteobacteria (31.42%) and Bacteroidetes (7.92%) constituted the major fraction of reads. Archaeal sequences contributed with no more than 0.6% to total reads in all studied samples. Apparently, the Mammoth Mountain exposure profile harbors insular microbial communities with specific structure that reflects the stratigraphy, properties and age.
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Affiliation(s)
- Andrey Rakitin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia.
| | - Aleksey Beletsky
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
| | - Andrey Mardanov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
| | - Natalya Surgucheva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
| | - Vladimir Sorokin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
| | | | - Anatoli Brouchkov
- Moscow State University, Leninskiye Gory 1, Moscow, 11999, Russia.,Tyumen State University, Volodarskogo St. 6, Tyumen, 625003, Russia
| | - Andrey Mulyukin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
| | - Svetlana Filippova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
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34
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Kulichevskaya IS, Naumoff DG, Ivanova AA, Rakitin AL, Dedysh SN. Detection of Chitinolytic Capabilities in the Freshwater Planctomycete Planctomicrobium piriforme. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719040076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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35
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Wieczorek AS, Schmidt O, Chatzinotas A, von Bergen M, Gorissen A, Kolb S. Ecological Functions of Agricultural Soil Bacteria and Microeukaryotes in Chitin Degradation: A Case Study. Front Microbiol 2019; 10:1293. [PMID: 31281293 PMCID: PMC6596343 DOI: 10.3389/fmicb.2019.01293] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/23/2019] [Indexed: 11/24/2022] Open
Abstract
Chitin provides a valuable carbon and nitrogen source for soil microorganisms and is a major component of particulate organic matter in agricultural soils. To date, there is no information on interaction and interdependence in chitin-degrading soil microbiomes. Since microbial chitin degradation occurs under both oxic and anoxic conditions and both conditions occur simultaneously in soil, the comparison of the active microbiome members under both conditions can reveal key players for the overall degradation in aerated soil. A time-resolved 16S rRNA stable isotope probing experiment was conducted with soil material from the top soil layer of a wheat-covered field. [13CU]-chitin was largely mineralized within 20 days under oxic conditions. Cellvibrio, Massilia, and several Bacteroidetes families were identified as initially active chitin degraders. Subsequently, Planctomycetes and Verrucomicrobia were labeled by assimilation of 13C carbon either from [13CU]-chitin or from 13C-enriched components of primary chitin degraders. Bacterial predators (e.g., Bdellovibrio and Bacteriovorax) were labeled, too, and non-labeled microeukaryotic predators (Alveolata) increased their relative abundance toward the end of the experiment (70 days), indicating that chitin degraders were subject to predation. Trophic interactions differed substantially under anoxic and oxic conditions. Various fermentation types occurred along with iron respiration. While Acidobacteria and Chloroflexi were the first taxa to be labeled, although at a low 13C level, Firmicutes and uncultured Bacteroidetes were predominantly labeled at a much higher 13C level during the later stages, suggesting that the latter two bacterial taxa were mainly responsible for the degradation of chitin and also provided substrates for iron reducers. Eventually, our study revealed that (1) hitherto unrecognized Bacteria were involved in a chitin-degrading microbial food web of an agricultural soil, (2) trophic interactions were substantially shaped by the oxygen availability, and (3) detectable predation was restricted to oxic conditions. The gained insights into trophic interactions foster our understanding of microbial chitin degradation, which is in turn crucial for an understanding of soil carbon dynamics.
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Affiliation(s)
- Adam S Wieczorek
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, University of Leipzig, Leipzig, Germany.,Department of Chemistry and Bioscience, University of Aalborg, Aalborg, Denmark
| | | | - Steffen Kolb
- Microbial Biogeochemistry, RA Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
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Korzhenkov AA, Toshchakov SV, Bargiela R, Gibbard H, Ferrer M, Teplyuk AV, Jones DL, Kublanov IV, Golyshin PN, Golyshina OV. Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity. MICROBIOME 2019; 7:11. [PMID: 30691532 PMCID: PMC6350386 DOI: 10.1186/s40168-019-0623-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 01/10/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND The current view suggests that in low-temperature acidic environments, archaea are significantly less abundant than bacteria. Thus, this study of the microbiome of Parys Mountain (Anglesey, UK) sheds light on the generality of this current assumption. Parys Mountain is a historically important copper mine and its acid mine drainage (AMD) water streams are characterised by constant moderate temperatures (8-18 °C), extremely low pH (1.7) and high concentrations of soluble iron and other metal cations. RESULTS Metagenomic and SSU rRNA amplicon sequencing of DNA from Parys Mountain revealed a significant proportion of archaea affiliated with Euryarchaeota, which accounted for ca. 67% of the community. Within this phylum, potentially new clades of Thermoplasmata were overrepresented (58%), with the most predominant group being "E-plasma", alongside low-abundant Cuniculiplasmataceae, 'Ca. Micrarchaeota' and 'Terrestrial Miscellaneous Euryarchaeal Group' (TMEG) archaea, which were phylogenetically close to Methanomassilicoccales and clustered with counterparts from acidic/moderately acidic settings. In the sediment, archaea and Thermoplasmata contributed the highest numbers in V3-V4 amplicon reads, in contrast with the water body community, where Proteobacteria, Nitrospirae, Acidobacteria and Actinobacteria outnumbered archaea. Cultivation efforts revealed the abundance of archaeal sequences closely related to Cuniculiplasma divulgatum in an enrichment culture established from the filterable fraction of the water sample. Enrichment cultures with unfiltered samples showed the presence of Ferrimicrobium acidiphilum, C. divulgatum, 'Ca. Mancarchaeum acidiphilum Mia14', 'Ca. Micrarchaeota'-related and diverse minor (< 2%) bacterial metagenomic reads. CONCLUSION Contrary to expectation, our study showed a high abundance of archaea in this extremely acidic mine-impacted environment. Further, archaeal populations were dominated by one particular group, suggesting that they are functionally important. The prevalence of archaea over bacteria in these microbiomes and their spatial distribution patterns represents a novel and important advance in our understanding of acidophile ecology. We also demonstrated a procedure for the specific enrichment of cell wall-deficient members of the archaeal component of this community, although the large fraction of archaeal taxa remained unculturable. Lastly, we identified a separate clustering of globally occurring acidophilic members of TMEG that collectively belong to a distinct order within Thermoplasmata with yet unclear functional roles in the ecosystem.
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Affiliation(s)
- Aleksei A. Korzhenkov
- National Research Center “Kurchatov Institute”, Akademika Kurchatova sq., 1, Moscow, 123182 Russia
| | - Stepan V. Toshchakov
- Winogradsky Institute of Microbiology, Federal Research Center for Biotechnology, Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/2, Moscow, 117312 Russia
| | - Rafael Bargiela
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
| | - Huw Gibbard
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
| | | | - Alina V. Teplyuk
- National Research Center “Kurchatov Institute”, Akademika Kurchatova sq., 1, Moscow, 123182 Russia
| | - David L. Jones
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
- UWA School of Agriculture and Environment, University of Western Australia, Crawley, WA 6009 Australia
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Federal Research Center for Biotechnology, Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/2, Moscow, 117312 Russia
| | - Peter N. Golyshin
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
- Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
| | - Olga V. Golyshina
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
- Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
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