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Structure and Function Analysis of Cultivated Meconopsis integrifolia Soil Microbial Community Based on High-Throughput Sequencing and Culturability. BIOLOGY 2023; 12:biology12020160. [PMID: 36829439 PMCID: PMC9952792 DOI: 10.3390/biology12020160] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/14/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023]
Abstract
(1) Background: The structure, function, and community interactions of soil microbial communities of cultivated Meconopsis integrifolia were characterized by studying this alpine flower and traditional endangered Tibetan medicine. (2) Methods: Soil bacteria and fungi were studied based on high-throughput sequencing technology. Bacteria were isolated using culturomics and functionally identified as IAA-producing, organic phosphorus-dissolving, inorganic phosphorus-dissolving, and iron-producing carriers. (3) Results: The dominant bacterial phyla were found to be Proteobacteria and Acidobacteria, and unclassified_Rhizobiales was the most abundant genus. Ascomycota and Mortierellomycota were the dominant fungal phyla. The bacteria were mainly carbon and nitrogen metabolizers, and the fungi were predominantly Saprotroph-Symbiotroph. The identified network was completely dominated by positive correlations, but the fungi were more complex than the bacteria, and the bacterial keystones were unclassified_Caulobacteraceae and Pedobacter. Most of the keystones of fungi belonged to the phyla Ascomycetes and Basidiomycota. The highest number of different species of culturable bacteria belonged to the genus Streptomyces, with three strains producing IAA, 12 strains solubilizing organic phosphorus, one strain solubilizing inorganic phosphorus, and nine strains producing iron carriers. (4) Conclusions: At the cost of reduced ecological stability, microbial communities increase cooperation toward promoting overall metabolic efficiency and enabling their survival in the extreme environment of the Tibetan Plateau. These pioneering results have value for the protection of endangered Meconopsis integrifolia under global warming and the sustainable utilization of its medicinal value.
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2
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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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3
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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: 196] [Impact Index Per Article: 49.0] [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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4
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Costa OYA, Oguejiofor C, Zühlke D, Barreto CC, Wünsche C, Riedel K, Kuramae EE. Impact of Different Trace Elements on the Growth and Proteome of Two Strains of Granulicella, Class "Acidobacteriia". Front Microbiol 2020; 11:1227. [PMID: 32625179 PMCID: PMC7315648 DOI: 10.3389/fmicb.2020.01227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/14/2020] [Indexed: 12/24/2022] Open
Abstract
Acidobacteria represents one of the most dominant bacterial groups across diverse ecosystems. However, insight into their ecology and physiology has been hampered by difficulties in cultivating members of this phylum. Previous cultivation efforts have suggested an important role of trace elements for the proliferation of Acidobacteria, however, the impact of these metals on their growth and metabolism is not known. In order to gain insight into this relationship, we evaluated the effect of trace element solution SL10 on the growth of two strains (5B5 and WH15) of Acidobacteria belonging to the genus Granulicella and studied the proteomic responses to manganese (Mn). Granulicella species had highest growth with the addition of Mn, as well as higher tolerance to this metal compared to seven other metal salts. Variations in tolerance to metal salt concentrations suggests that Granulicella sp. strains possess different mechanisms to deal with metal ion homeostasis and stress. Furthermore, Granulicella sp. 5B5 might be more adapted to survive in an environment with higher concentration of several metal ions when compared to Granulicella sp. WH15. The proteomic profiles of both strains indicated that Mn was more important in enhancing enzymatic activity than to protein expression regulation. In the genomic analyses, we did not find the most common transcriptional regulation of Mn homeostasis, but we found candidate transporters that could be potentially involved in Mn homeostasis for Granulicella species. The presence of such transporters might be involved in tolerance to higher Mn concentrations, improving the adaptability of bacteria to metal enriched environments, such as the decaying wood-rich Mn environment from which these two Granulicella strains were isolated.
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Affiliation(s)
- Ohana Y A Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Chidinma Oguejiofor
- Department of Soil Science and Meteorology, Michael Okpara University of Agriculture, Umudike, Nigeria
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Cristine C Barreto
- Genomic Sciences and Biotechnology Program, Catholic University of Brasilia, Distrito Federal, Brazil
| | - Christine Wünsche
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
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5
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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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Costa OY, Zerillo MM, Zühlke D, Kielak AM, Pijl A, Riedel K, Kuramae EE. Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses. Microorganisms 2020; 8:E244. [PMID: 32059463 PMCID: PMC7074687 DOI: 10.3390/microorganisms8020244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/08/2020] [Accepted: 02/10/2020] [Indexed: 01/18/2023] Open
Abstract
The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin-antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.
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Affiliation(s)
- Ohana Y.A. Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Marcelo M. Zerillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17487 Greifswald, Germany; (D.Z.); (K.R.)
| | - Anna M. Kielak
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Agata Pijl
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17487 Greifswald, Germany; (D.Z.); (K.R.)
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
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7
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D'Auria G, Artacho A, Rojas RA, Bautista JS, Méndez R, Gamboa MT, Gamboa JR, Gómez-Cruz R. Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs. Genes (Basel) 2018; 9:E55. [PMID: 29361802 PMCID: PMC5793206 DOI: 10.3390/genes9010055] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/12/2018] [Accepted: 01/13/2018] [Indexed: 01/22/2023] Open
Abstract
New biotechnology applications require in-depth preliminary studies of biodiversity. The methods of massive sequencing using metagenomics and bioinformatics tools offer us sufficient and reliable knowledge to understand environmental diversity, to know new microorganisms, and to take advantage of their functional genes. Villa Luz caves, in the southern Mexican state of Tabasco, are fed by at least 26 groundwater inlets, containing 300-500 mg L-1 H2S and <0.1 mg L-1 O2. We extracted environmental DNA for metagenomic analysis of collected samples in five selected Villa Luz caves sites, with pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4. These include: biovermiculites, a bacterial association that can grow on the rock walls; snottites, that are whitish, viscous biofilms hanging from the rock walls, and sacks or bags of phlegm, which live within the aquatic environment of the springs. Through the emergency food assistance program (TEFAP) pyrosequencing, a total of 20,901 readings of amplification products from hypervariable regions V1 and V3 of 16S rRNA bacterial gene in whole and pure metagenomic DNA samples were generated. Seven bacterial phyla were identified. As a result, Proteobacteria was more frequent than Acidobacteria. Finally, acidophilic Proteobacteria was detected in UJAT5 sample.
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Affiliation(s)
- Giuseppe D'Auria
- Sequencing and Bioinformatics Service, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia 46020.
| | - Alejandro Artacho
- Center for Advanced Research in Public Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia 46020.
| | - Rafael A Rojas
- Chemical Engineering Faculty, Exact Sciences and Engineering Campus, Autonomous University of Yucatán (UADY), Mérida, Yucatán 97050..
| | - José S Bautista
- Biological Sciences Academic Division, Autonomous University Juárez de Tabasco (UJAT), Villahermosa, Centro, Tabasco 99630, Mexico.
| | - Roberto Méndez
- Biological Sciences Academic Division, Autonomous University Juárez de Tabasco (UJAT), Villahermosa, Centro, Tabasco 99630, Mexico.
| | - María T Gamboa
- Biological Sciences Academic Division, Autonomous University Juárez de Tabasco (UJAT), Villahermosa, Centro, Tabasco 99630, Mexico.
| | - Jesús R Gamboa
- Biological Sciences Academic Division, Autonomous University Juárez de Tabasco (UJAT), Villahermosa, Centro, Tabasco 99630, Mexico.
| | - Rodolfo Gómez-Cruz
- Biological Sciences Academic Division, Autonomous University Juárez de Tabasco (UJAT), Villahermosa, Centro, Tabasco 99630, Mexico.
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Han C, Wang Z, Si G, Lei T, Yuan Y, Zhang G. Increased precipitation accelerates soil organic matter turnover associated with microbial community composition in topsoil of alpine grassland on the eastern Tibetan Plateau. Can J Microbiol 2017; 63:811-821. [PMID: 28742981 DOI: 10.1139/cjm-2017-0157] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Large quantities of carbon are stored in alpine grassland of the Tibetan Plateau, which is extremely sensitive to climate change. However, it remains unclear whether soil organic matter (SOM) in different layers responds to climate change analogously, and whether microbial communities play vital roles in SOM turnover of topsoil. In this study we measured and collected SOM turnover by the 14C method in alpine grassland to test climatic effects on SOM turnover in soil profiles. Edaphic properties and microbial communities in the northwestern Qinghai Lake were investigated to explore microbial influence on SOM turnover. SOM turnover in surface soil (0-10 cm) was more sensitive to precipitation than that in subsurface layers (10-40 cm). Precipitation also imposed stronger effects on the composition of microbial communities in the surface layer than that in deeper soil. At the 5-10 cm depth, the SOM turnover rate was positively associated with the bacteria/fungi biomass ratio and the relative abundance of Acidobacteria, both of which are related to precipitation. Partial correlation analysis suggested that increased precipitation could accelerate the SOM turnover rate in topsoil by structuring soil microbial communities. Conversely, carbon stored in deep soil would be barely affected by climate change. Our results provide valuable insights into the dynamics and storage of SOM in alpine grasslands under future climate scenarios.
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Affiliation(s)
- Conghai Han
- a Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.,b University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Zongli Wang
- c Key Laboratory of Western China's Environmental Systems, Lanzhou University, Lanzhou 730000, Gansu, People's Republic of China
| | - Guicai Si
- d Key Laboratory of Petroleum Resources, Gansu Province/Key Laboratory of Petroleum Resources Research, Institute of Geology and Geophysics, Chinese Academy of Sciences, Lanzhou 730000, Gansu, People's Republic of China
| | - Tianzhu Lei
- d Key Laboratory of Petroleum Resources, Gansu Province/Key Laboratory of Petroleum Resources Research, Institute of Geology and Geophysics, Chinese Academy of Sciences, Lanzhou 730000, Gansu, People's Republic of China
| | - Yanli Yuan
- a Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Gengxin Zhang
- a Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
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9
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Wegner CE, Liesack W. Unexpected Dominance of Elusive Acidobacteria in Early Industrial Soft Coal Slags. Front Microbiol 2017; 8:1023. [PMID: 28642744 PMCID: PMC5462947 DOI: 10.3389/fmicb.2017.01023] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/22/2017] [Indexed: 11/19/2022] Open
Abstract
Acid mine drainage (AMD) and mine tailing environments are well-characterized ecosystems known to be dominated by organisms involved in iron- and sulfur-cycling. Here we examined the microbiology of industrial soft coal slags that originate from alum leaching, an ecosystem distantly related to AMD environments. Our study involved geochemical analyses, bacterial community profiling, and shotgun metagenomics. The slags still contained high amounts of alum constituents (aluminum, sulfur), which mediated direct and indirect effects on bacterial community structure. Bacterial groups typically found in AMD systems and mine tailings were not present. Instead, the soft coal slags were dominated by uncharacterized groups of Acidobacteria (DA052 [subdivision 2], KF-JG30-18 [subdivision 13]), Actinobacteria (TM214), Alphaproteobacteria (DA111), and Chloroflexi (JG37-AG-4), which have previously been detected primarily in peatlands and uranium waste piles. Shotgun metagenomics allowed us to reconstruct 13 high-quality Acidobacteria draft genomes, of which two genomes could be directly linked to dominating groups (DA052, KF-JG30-18) by recovered 16S rRNA gene sequences. Comparative genomics revealed broad carbon utilization capabilities for these two groups of elusive Acidobacteria, including polysaccharide breakdown (cellulose, xylan) and the competence to metabolize C1 compounds (ribulose monophosphate pathway) and lignin derivatives (dye-decolorizing peroxidases). Equipped with a broad range of efflux systems for metal cations and xenobiotics, DA052 and KF-JG30-18 may have a competitive advantage over other bacterial groups in this unique habitat.
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Affiliation(s)
- Carl-Eric Wegner
- Department of Biogeochemistry, Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University JenaJena, Germany
| | - Werner Liesack
- Department of Biogeochemistry, Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
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10
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Kielak AM, Barreto CC, Kowalchuk GA, van Veen JA, Kuramae EE. The Ecology of Acidobacteria: Moving beyond Genes and Genomes. Front Microbiol 2016; 7:744. [PMID: 27303369 PMCID: PMC4885859 DOI: 10.3389/fmicb.2016.00744] [Citation(s) in RCA: 426] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 05/03/2016] [Indexed: 12/01/2022] Open
Abstract
The phylum Acidobacteria is one of the most widespread and abundant on the planet, yet remarkably our knowledge of the role of these diverse organisms in the functioning of terrestrial ecosystems remains surprisingly rudimentary. This blatant knowledge gap stems to a large degree from the difficulties associated with the cultivation of these bacteria by classical means. Given the phylogenetic breadth of the Acidobacteria, which is similar to the metabolically diverse Proteobacteria, it is clear that detailed and functional descriptions of acidobacterial assemblages are necessary. Fortunately, recent advances are providing a glimpse into the ecology of members of the phylum Acidobacteria. These include novel cultivation and enrichment strategies, genomic characterization and analyses of metagenomic DNA from environmental samples. Here, we couple the data from these complementary approaches for a better understanding of their role in the environment, thereby providing some initial insights into the ecology of this important phylum. All cultured acidobacterial type species are heterotrophic, and members of subdivisions 1, 3, and 4 appear to be more versatile in carbohydrate utilization. Genomic and metagenomic data predict a number of ecologically relevant capabilities for some acidobacteria, including the ability to: use of nitrite as N source, respond to soil macro-, micro nutrients and soil acidity, express multiple active transporters, degrade gellan gum and produce exopolysaccharide (EPS). Although these predicted properties allude to a competitive life style in soil, only very few of these prediction shave been confirmed via physiological studies. The increased availability of genomic and physiological information, coupled to distribution data in field surveys and experiments, should direct future progress in unraveling the ecology of this important but still enigmatic phylum.
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Affiliation(s)
- Anna M Kielak
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
| | - Cristine C Barreto
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília Brasília, Brazil
| | - George A Kowalchuk
- Ecology and Biodiversity Group, University of Utrecht Utrecht, Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
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11
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Leung HTC, Maas KR, Wilhelm RC, Mohn WW. Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils. THE ISME JOURNAL 2016; 10:363-75. [PMID: 26274049 PMCID: PMC4737928 DOI: 10.1038/ismej.2015.118] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 06/03/2015] [Accepted: 06/04/2015] [Indexed: 11/09/2022]
Abstract
Forest ecosystems need to be sustainably managed, as they are major reservoirs of biodiversity, provide important economic resources and modulate global climate. We have a poor knowledge of populations responsible for key biomass degradation processes in forest soils and the effects of forest harvesting on these populations. Here, we investigated the effects of three timber-harvesting methods, varying in the degree of organic matter removal, on putatively hemicellulolytic bacterial and fungal populations 10 or more years after harvesting and replanting. We used stable-isotope probing to identify populations that incorporated (13)C from labeled hemicellulose, analyzing (13)C-enriched phospholipid fatty acids, bacterial 16 S rRNA genes and fungal ITS regions. In soil microcosms, we identified 104 bacterial and 52 fungal hemicellulolytic operational taxonomic units (OTUs). Several of these OTUs are affiliated with taxa not previously reported to degrade hemicellulose, including the bacterial genera Methylibium, Pelomonas and Rhodoferax, and the fungal genera Cladosporium, Pseudeurotiaceae, Capronia, Xenopolyscytalum and Venturia. The effect of harvesting on hemicellulolytic populations was evaluated based on in situ bacterial and fungal OTUs. Harvesting treatments had significant but modest long-term effects on relative abundances of hemicellulolytic populations, which differed in strength between two ecozones and between soil layers. For soils incubated in microcosms, prior harvesting treatments did not affect the rate of incorporation of hemicellulose carbon into microbial biomass. In six ecozones across North America, distributions of the bacterial hemicellulolytic OTUs were similar, whereas distributions of fungal ones differed. Our work demonstrates that diverse taxa in soil are hemicellulolytic, many of which are differentially affected by the impact of harvesting on environmental conditions. However, the hemicellulolytic capacity of soil communities appears resilient.
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Affiliation(s)
- Hilary T C Leung
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kendra R Maas
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Roland C Wilhelm
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - William W Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
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Navarrete AA, Venturini AM, Meyer KM, Klein AM, Tiedje JM, Bohannan BJM, Nüsslein K, Tsai SM, Rodrigues JLM. Differential Response of Acidobacteria Subgroups to Forest-to-Pasture Conversion and Their Biogeographic Patterns in the Western Brazilian Amazon. Front Microbiol 2015; 6:1443. [PMID: 26733981 PMCID: PMC4686610 DOI: 10.3389/fmicb.2015.01443] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/03/2015] [Indexed: 11/13/2022] Open
Abstract
Members of the phylum Acidobacteria are among the most abundant soil bacteria on Earth, but little is known about their response to environmental changes. We asked how the relative abundance and biogeographic patterning of this phylum and its subgroups responded to forest-to-pasture conversion in soils of the western Brazilian Amazon. Pyrosequencing of 16S rRNA genes was employed to assess the abundance and composition of the Acidobacteria community across 54 soil samples taken using a spatially nested sampling scheme at the landscape level. Numerically, Acidobacteria represented 20% of the total bacterial community in forest soils and 11% in pasture soils. Overall, 15 different Acidobacteria subgroups of the current 26 subgroups were detected, with Acidobacteria subgroups 1, 3, 5, and 6 accounting together for 87% of the total Acidobacteria community in forest soils and 75% in pasture soils. Concomitant with changes in soil chemistry after forest-to-pasture conversion—particularly an increase in properties linked to soil acidity and nutrient availability—we observed an increase in the relative abundances of Acidobacteria subgroups 4, 10, 17, and 18, and a decrease in the relative abundances of other Acidobacteria subgroups in pasture relative to forest soils. The composition of the total Acidobacteria community as well as the most abundant Acidobacteria subgroups (1, 3, 5, and 6) was significantly more similar in composition across space in pasture soils than in forest soils. These results suggest that preponderant responses of Acidobacteria subgroups, especially subgroups 1, 3, 4, 5, and 6, to forest-to-pasture conversion effects in soils could be used to define management-indicators of agricultural practices in the Amazon Basin. These acidobacterial responses are at least in part through alterations on acidity- and nutrient-related properties of the Amazon soils.
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Affiliation(s)
- Acacio A Navarrete
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo Piracicaba, Brazil
| | - Andressa M Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo Piracicaba, Brazil
| | - Kyle M Meyer
- Department of Biology, Institute of Ecology and Evolution, University of Oregon Eugene, OR, USA
| | - Ann M Klein
- Department of Biology, Institute of Ecology and Evolution, University of Oregon Eugene, OR, USA
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Center for Microbial Ecology, Michigan State University East Lansing, MI, USA
| | - Brendan J M Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon Eugene, OR, USA
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo Piracicaba, Brazil
| | - Jorge L M Rodrigues
- Department of Land, Air and Water Resources, University of California, Davis Davis, CA, USA
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