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Koner S, Chen JS, Rathod J, Hussain B, Hsu BM. Unravelling the ultramafic rock-driven serpentine soil formation leading to the geo-accumulation of heavy metals: An impact on the resident microbiome, biogeochemical cycling and acclimatized eco-physiological profiles. ENVIRONMENTAL RESEARCH 2023; 216:114664. [PMID: 36336091 DOI: 10.1016/j.envres.2022.114664] [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: 09/01/2022] [Revised: 10/13/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
In the present study, we have underpinned the serpentine rock, serpentinized ultramafic soil and rhizosphere's microbial communities, signifying their heavy metals-exposed taxa signatures and functional repertoires in comparison to non-serpentine soils. The results revealed that the serpentine rock embedded soil highlighted the geo-accumulation of higher amount of Cr and Ni impacting soil microbial diversity negatively by metal stress-driven selection. Biolog Ecoplate CLPP defined a restricted spectrum of C-utilization in the higher heavy metal-containing serpentine samples compared to non-serpentine. The linear discriminant analysis (LDA) score identified a higher abundance of Desulfobacterota, Opitutales, and Bacteroidales in low Cr and Ni-stressed non-serpentine-exposed samples. Whereas the abundance of Propionibacteriales and Actinobacteriota were significantly enriched in the serpentine niche. Further, the C, N, S, Fe, and methane biogeochemical cycles linked functional members were identified, and showing higher functional diversity in low Cr and Ni concentration-containing rhizosphere JS-soils. The Pearson correlation coefficient (r) value confirmed the abundance of functional members linked to specific biogeochemical cycle, positively correlated with relevant pathway enrichment. Ultimately, this study highlighted the heavy metal stress within a serpentine setting that could limit the resident microbial community's metabolic diversity and further select the bacteria that could thrive in the serpentine-associated heavy metal-stressed soils. These acclimatized microbes could pave the way for the future applications in the soil conservation and management.
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Affiliation(s)
- Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung, Taiwan
| | - Jagat Rathod
- Department of Environmental Biotechnology, Gujarat Biotechnology University, Near Gujarat International Finance and Tec (GIFT)-City, Gandhinagar, 382355, Gujarat, India
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Center for Innovative on Aging Society, National Chung Cheng University, Chiayi County, Taiwan.
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2
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Lopez S, Morel JL, Benizri E. The parameters determining hyperaccumulator rhizobacteria diversity depend on the study scale. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155274. [PMID: 35452722 DOI: 10.1016/j.scitotenv.2022.155274] [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: 11/09/2021] [Revised: 03/23/2022] [Accepted: 04/10/2022] [Indexed: 06/14/2023]
Abstract
Soils harbor some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. Numerous parameters, intrinsic to plant physiology, life history and the soil itself, can influence the structure of rhizomicrobial communities. While our knowledge of rhizosphere microbial diversity is increasing, opinion is divided as to whether the factors that most impact this diversity are abiotic, climatic or plant selection. Here we focused on the rhizosphere bacterial diversity of nickel hyperaccumulator plants (28 species from Mediterranean or tropical climates). We showed, by leveraging 16S Illumina sequencing of 153 ultramafic rhizosphere soils, that bacterial genetic diversity was highest in Mediterranean habitats where plant diversity was the lowest. Concerning those parameters driving this diversity, we demonstrated that climate drives bacterial diversity, in particular with the annual temperature variation. Focusing on each region, we underlined the substantial role of soil physicochemical parameters. Our results highlight the importance of considering spatial scale when explaining bacterial community diversity.
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Affiliation(s)
- Séverine Lopez
- INRAE, Bordeaux Sciences Agro, ISVV, SAVE, F-33140 Villenave d'Ornon, France; Université de Lorraine, INRAE, Laboratoire Sols et Environnement, 54000 Nancy, France
| | - Jean Louis Morel
- Université de Lorraine, INRAE, Laboratoire Sols et Environnement, 54000 Nancy, France
| | - Emile Benizri
- Université de Lorraine, INRAE, Laboratoire Sols et Environnement, 54000 Nancy, France.
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3
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Nagarajan V, Tsai HC, Chen JS, Hussain B, Koner S, Hseu ZY, Hsu BM. Comparison of bacterial communities and their functional profiling using 16S rRNA gene sequencing between the inherent serpentine-associated sites, hyper-accumulator, downgradient agricultural farmlands, and distal non-serpentine soils. JOURNAL OF HAZARDOUS MATERIALS 2022; 431:128557. [PMID: 35247742 DOI: 10.1016/j.jhazmat.2022.128557] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/25/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
This study aims to determine and compare the bacterial community and functional profiles associated with serpentine sites, innate hyper-accumulating weed, downgradient agricultural farmlands and non-serpentine sites using 16S rRNA gene sequencing. Elemental analysis revealed that the serpentine rock and weathered soil have higher magnesium, nickel, chromium, magnesium/calcium and lower calcium/magnesium ratios and agricultural farmlands have recorded elevated chromium. Proteobacteria were found predominant, except the non-serpentine site which was rich in Cyanobacteria. PCA analysis at the genus level indicates the uniqueness of different experimental groups, except the hyperaccumulators which exhibited relatively less dissimilarity. The shift analysis showed the serpentine sites were characterized by the abundance of bacteria having heavy metal effluxion. The hyper-accumulating weeds were higher in plant growth-promoting bacteria expressing tolerance against heavy metals toxicity such as nickel, chromium, cobalt and arsenic. Besides, the agricultural lands were abundant in wetland-associated methanogens and metal (manganese, iron and zinc) transporting function related bacteria. The results suggest that the inherent edaphic factors including heavy metal content, the interacting behavior of hyperaccumulator's rhizosphere microbiota with soil and anthropogenic activities such as agricultural practices could be a major determinant of the variation in the bacterial community selection and abundance in the respective study sites.
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Affiliation(s)
- Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien, Taiwan; Department of Psychiatry, Tzu-Chi General Hospital, Hualien, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Zeng-Yei Hseu
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan.
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4
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Igwe AN, Quasem B, Liu N, Vannette RL. Plant phenology influences rhizosphere microbial community and is accelerated by serpentine microorganisms in Plantago erecta. FEMS Microbiol Ecol 2021; 97:6300443. [PMID: 34132353 DOI: 10.1093/femsec/fiab085] [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: 03/23/2021] [Accepted: 06/14/2021] [Indexed: 11/14/2022] Open
Abstract
Serpentine soils are drought-prone and rich in heavy metals, and plants growing on serpentine soils host distinct microbial communities that may affect plant survival and phenotype. However, whether the rhizosphere communities of plants from different soil chemistries are initially distinct or diverge over time may help us understand drivers of microbial community structure and function in stressful soils. Here, we test the hypothesis that rhizosphere microbial communities will converge over time (plant development), independent of soil chemistry and microbial source. We grew Plantago erecta in serpentine or nonserpentine soil, with serpentine or nonserpentine microbes and tracked plant growth and root phenotypes. We used 16S rRNA gene barcoding to compare bacterial species composition at seedling, vegetative, early- and late-flowering phases. Plant phenotype and rhizosphere bacterial communities were mainly structured by soil type, with minor contributions by plant development, microbe source and their interactions. Serpentine microorganisms promoted early flowering in plants on nonserpentine soils. Despite strong effects of soil chemistry, the convergence in bacterial community composition across development demonstrates the importance of the plant-microbe interactions in shaping microbial assembly processes across soil types.
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Affiliation(s)
- Alexandria N Igwe
- University of Miami, Department of Biology, 1301 Memorial Drive, Coral Gables, FL 33146, USA
| | - Bibi Quasem
- University of California, Davis, Department of Entomology and Nematology, One Shields Avenue, Davis, CA 95616, USA
| | - Naomi Liu
- University of California, Davis, Department of Entomology and Nematology, One Shields Avenue, Davis, CA 95616, USA
| | - Rachel L Vannette
- University of California, Davis, Department of Entomology and Nematology, One Shields Avenue, Davis, CA 95616, USA
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5
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Konečná V, Yant L, Kolář F. The Evolutionary Genomics of Serpentine Adaptation. FRONTIERS IN PLANT SCIENCE 2020; 11:574616. [PMID: 33391295 PMCID: PMC7772150 DOI: 10.3389/fpls.2020.574616] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Serpentine barrens are among the most challenging settings for plant life. Representing a perfect storm of hazards, serpentines consist of broadly skewed elemental profiles, including abundant toxic metals and low nutrient contents on drought-prone, patchily distributed substrates. Accordingly, plants that can tolerate the challenges of serpentine have fascinated biologists for decades, yielding important insights into adaptation to novel ecologies through physiological change. Here we highlight recent progress from studies which demonstrate the power of serpentine as a model for the genomics of adaptation. Given the moderate - but still tractable - complexity presented by the mix of hazards on serpentine, these venues are well-suited for the experimental inquiry of adaptation both in natural and manipulated conditions. Moreover, the island-like distribution of serpentines across landscapes provides abundant natural replicates, offering power to evolutionary genomic inference. Exciting recent insights into the genomic basis of serpentine adaptation point to a partly shared basis that involves sampling from common allele pools available from retained ancestral polymorphism or via gene flow. However, a lack of integrated studies deconstructing complex adaptations and linking candidate alleles with fitness consequences leaves room for much deeper exploration. Thus, we still seek the crucial direct link between the phenotypic effect of candidate alleles and their measured adaptive value - a prize that is exceedingly rare to achieve in any study of adaptation. We expect that closing this gap is not far off using the promising model systems described here.
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Affiliation(s)
- Veronika Konečná
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Pru˚honice, Czechia
| | - Levi Yant
- Future Food Beacon and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Pru˚honice, Czechia
- Natural History Museum, University of Oslo, Oslo, Norway
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Khilyas IV, Sorokina AV, Elistratova AA, Markelova MI, Siniagina MN, Sharipova MR, Shcherbakova TA, D’Errico ME, Cohen MF. Microbial diversity and mineral composition of weathered serpentine rock of the Khalilovsky massif. PLoS One 2019; 14:e0225929. [PMID: 31830070 PMCID: PMC6907791 DOI: 10.1371/journal.pone.0225929] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/15/2019] [Indexed: 01/17/2023] Open
Abstract
Endolithic microbial communities survive nutrient and energy deficient conditions while contributing to the weathering of their mineral substrate. This study examined the mineral composition and microbial communities of fully serpentinized weathered rock from 0.1 to 6.5 m depth at a site within the Khalilovsky massif, Orenburg Region, Southern Ural Mountains, Russia. The mineral composition includes a major content of serpentinite family (mostly consisting of lizardite and chrysotile), magnesium hydrocarbonates (hydromagnesite with lesser amounts of hydrotalcite and pyroaurite) concentrated in the upper layers, and clay minerals. We found that the deep-seated weathered serpentinites are chrysotile-type minerals, while the middle and surface serpentinites mostly consist of lizardite and chrysotile types. Microbial community analysis, based on 16S rRNA gene sequencing, showed a similar diversity of phyla throughout the depth profile. The dominant bacterial phyla were the Actinobacteria (of which unclassified genera in the orders Acidimicrobiales and Actinomycetales were most numerous), Chloroflexi (dominated by an uncultured P2-11E order) and the Proteobacteria (predominantly class Betaproteobacteria). Densities of several groups of bacteria were negatively correlated with depth. Occurrence of the orders Actinomycetales, Gaiellales, Solirubrobacterales, Rhizobiales and Burkholderiales were positively correlated with depth. Our findings show that endolithic microbial communities of the Khalilovsky massif have similar diversity to those of serpentine soils and rocks, but are substantially different from those of the aqueous environments of actively serpentinizing systems.
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Affiliation(s)
- Irina V. Khilyas
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
- * E-mail:
| | - Alyona V. Sorokina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Anna A. Elistratova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Maria I. Markelova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Maria N. Siniagina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Margarita R. Sharipova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Tatyana A. Shcherbakova
- FSUE Central Research Institute of Geology of Non-metallic Mineral Resources, Kazan, Russian Federation
| | - Megan E. D’Errico
- School of Science and Technology, Sonoma State University, Rohnert Park, CA, United States of America
| | - Michael F. Cohen
- Department of Biology, Sonoma State University, Rohnert Park, CA, United States of America
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7
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Costa FS, Macedo MWFS, Araújo ACM, Rodrigues CA, Kuramae EE, de Barros Alcanfor SK, Pessoa-Filho M, Barreto CC. Assessing nickel tolerance of bacteria isolated from serpentine soils. Braz J Microbiol 2019; 50:705-713. [PMID: 31297747 DOI: 10.1007/s42770-019-00111-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 06/11/2019] [Indexed: 10/26/2022] Open
Abstract
Serpentine soils present unique characteristics such as a low Ca/Mg ratio, low concentration of nutrients, and a high concentration of heavy metals, especially nickel. Soil bacterial isolates from an ultramafic complex located in the tropical savanna known as the Brazilian Cerrado were studied. Nickel-tolerant bacteria were obtained, and their ability to remove nickel from a culture medium was assessed. Bacterial isolates presented higher tolerance to nickel salts than previously reported for bacteria obtained from serpentine environments in other regions of the world. In addition, the quantification of nickel in cell pellets indicated that at least four isolates may adsorb soluble forms of nickel. It is expected that information gathered in this study will support future efforts to exploit serpentine soil bacteria for biotechnological processes involving nickel decontamination from environmental samples.
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Affiliation(s)
- Flávio Silva Costa
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, SGAN 916, Avenida W5, Brasilia, 70790-160, Brazil.,Institute of Microbiology, Friedrich-Schiller-Universität Jena, Neugasse 25, 07743, Jena, Germany
| | - Maria Wanna Figueiredo Sena Macedo
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, SGAN 916, Avenida W5, Brasilia, 70790-160, Brazil
| | - Ana Carolina Moreira Araújo
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, SGAN 916, Avenida W5, Brasilia, 70790-160, Brazil
| | - Cassimira Albuquerque Rodrigues
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, SGAN 916, Avenida W5, Brasilia, 70790-160, Brazil
| | - Eiko Eurya Kuramae
- Department of Microbial Ecology, Nederlands Instituut vor Ecologie (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | | | - Marco Pessoa-Filho
- Embrapa Cerrados, BR 020, Km 18, PO Box 08223, Brasilia, 73310-970, Brazil
| | - Cristine Chaves Barreto
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, SGAN 916, Avenida W5, Brasilia, 70790-160, Brazil.
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8
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The Role of the Rhizosphere and Microbes Associated with Hyperaccumulator Plants in Metal Accumulation. AGROMINING: FARMING FOR METALS 2018. [DOI: 10.1007/978-3-319-61899-9_9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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9
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The Influence of the Host Plant Is the Major Ecological Determinant of the Presence of Nitrogen-Fixing Root Nodule Symbiont Cluster II Frankia Species in Soil. Appl Environ Microbiol 2016; 83:AEM.02661-16. [PMID: 27795313 DOI: 10.1128/aem.02661-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/07/2016] [Indexed: 12/21/2022] Open
Abstract
The actinobacterial genus Frankia establishes nitrogen-fixing root nodule symbioses with specific hosts within the nitrogen-fixing plant clade. Of four genetically distinct subgroups of Frankia, cluster I, II, and III strains are capable of forming effective nitrogen-fixing symbiotic associations, while cluster IV strains generally do not. Cluster II Frankia strains have rarely been detected in soil devoid of host plants, unlike cluster I or III strains, suggesting a stronger association with their host. To investigate the degree of host influence, we characterized the cluster II Frankia strain distribution in rhizosphere soil in three locations in northern California. The presence/absence of cluster II Frankia strains at a given site correlated significantly with the presence/absence of host plants on the site, as determined by glutamine synthetase (glnA) gene sequence analysis, and by microbiome analysis (16S rRNA gene) of a subset of host/nonhost rhizosphere soils. However, the distribution of cluster II Frankia strains was not significantly affected by other potential determinants such as host-plant species, geographical location, climate, soil pH, or soil type. Rhizosphere soil microbiome analysis showed that cluster II Frankia strains occupied only a minute fraction of the microbiome even in the host-plant-present site and further revealed no statistically significant difference in the α-diversity or in the microbiome composition between the host-plant-present or -absent sites. Taken together, these data suggest that host plants provide a factor that is specific for cluster II Frankia strains, not a general growth-promoting factor. Further, the factor accumulates or is transported at the site level, i.e., beyond the host rhizosphere. IMPORTANCE Biological nitrogen fixation is a bacterial process that accounts for a major fraction of net new nitrogen input in terrestrial ecosystems. Transfer of fixed nitrogen to plant biomass is especially efficient via root nodule symbioses, which represent evolutionarily and ecologically specialized mutualistic associations. Frankia spp. (Actinobacteria), especially cluster II Frankia spp., have an extremely broad host range, yet comparatively little is known about the soil ecology of these organisms in relation to the host plants and their rhizosphere microbiomes. This study reveals a strong influence of the host plant on soil distribution of cluster II Frankia spp.
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10
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Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach. PLoS One 2016. [PMID: 27907121 DOI: 10.1371/journal.pone.0167405,] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity. Therefore, four plant formation types at two distinct sites were studied. These formations represent different stages in a potential chronosequence. Soil cores, according to a given sampling procedure, were collected to assess microbial diversity using a metagenomic approach, and to characterise the physico-chemical parameters. A botanical inventory was also performed. Our results indicated that microbial richness, composition and abundance were linked to the plant cover type and the dominant plant species. Furthermore, a large proportion of Ascomycota phylum (fungi), mostly in non-rainforest formations, and Planctomycetes phylum (bacteria) in all formations were observed. Interestingly, such patterns could be indicators of past disturbances that occurred on different time scales. Furthermore, the bacteria and fungi were influenced by diverse edaphic parameters as well as by the interplay between these two soil communities. Another striking finding was the existence of a site effect. Differences in microbial communities between geographical locations may be explained by dispersal limitation in the context of the biogeographical island theory. In conclusion, each plant formation at each site possesses is own microbial community resulting from multiple interactions between abiotic and biotic factors.
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11
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Gourmelon V, Maggia L, Powell JR, Gigante S, Hortal S, Gueunier C, Letellier K, Carriconde F. Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach. PLoS One 2016; 11:e0167405. [PMID: 27907121 PMCID: PMC5131939 DOI: 10.1371/journal.pone.0167405] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/14/2016] [Indexed: 11/30/2022] Open
Abstract
Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity. Therefore, four plant formation types at two distinct sites were studied. These formations represent different stages in a potential chronosequence. Soil cores, according to a given sampling procedure, were collected to assess microbial diversity using a metagenomic approach, and to characterise the physico-chemical parameters. A botanical inventory was also performed. Our results indicated that microbial richness, composition and abundance were linked to the plant cover type and the dominant plant species. Furthermore, a large proportion of Ascomycota phylum (fungi), mostly in non-rainforest formations, and Planctomycetes phylum (bacteria) in all formations were observed. Interestingly, such patterns could be indicators of past disturbances that occurred on different time scales. Furthermore, the bacteria and fungi were influenced by diverse edaphic parameters as well as by the interplay between these two soil communities. Another striking finding was the existence of a site effect. Differences in microbial communities between geographical locations may be explained by dispersal limitation in the context of the biogeographical island theory. In conclusion, each plant formation at each site possesses is own microbial community resulting from multiple interactions between abiotic and biotic factors.
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Affiliation(s)
- Véronique Gourmelon
- Institut Agronomique néo-Calédonien (IAC), Axe 2 "Diversités biologique et fonctionnelle des écosystèmes terrestres", Nouméa, New Caledonia
| | - Laurent Maggia
- Institut Agronomique néo-Calédonien (IAC), Axe 2 "Diversités biologique et fonctionnelle des écosystèmes terrestres", Nouméa, New Caledonia.,CIRAD, UMR AGAP, Nouméa, New Caledonia
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Sarah Gigante
- Institut Agronomique néo-Calédonien (IAC), Axe 2 "Diversités biologique et fonctionnelle des écosystèmes terrestres", Nouméa, New Caledonia
| | - Sara Hortal
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Claire Gueunier
- Société Le Nickel (SLN) - Groupe ERAMET, Département Environnement, Nouméa, New Caledonia
| | - Kelly Letellier
- Institut Agronomique néo-Calédonien (IAC), Axe 2 "Diversités biologique et fonctionnelle des écosystèmes terrestres", Nouméa, New Caledonia
| | - Fabian Carriconde
- Institut Agronomique néo-Calédonien (IAC), Axe 2 "Diversités biologique et fonctionnelle des écosystèmes terrestres", Nouméa, New Caledonia
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12
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Pessoa-Filho M, Barreto CC, dos Reis Junior FB, Fragoso RR, Costa FS, de Carvalho Mendes I, de Andrade LRM. Microbiological functioning, diversity, and structure of bacterial communities in ultramafic soils from a tropical savanna. Antonie van Leeuwenhoek 2015; 107:935-49. [PMID: 25616909 DOI: 10.1007/s10482-015-0386-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 01/13/2015] [Indexed: 12/01/2022]
Abstract
Ultramafic soils are characterized by high levels of metals, and have been studied because of their geochemistry and its relation to their biological component. This study evaluated soil microbiological functioning (SMF), richness, diversity, and structure of bacterial communities from two ultramafic soils and from a non-ultramafic soil in the Brazilian Cerrado, a tropical savanna. SMF was represented according to simultaneous analysis of microbial biomass C (MBC) and activities of the enzymes β-glucosidase, acid phosphomonoesterase and arylsulfatase, linked to the C, P and S cycles. Bacterial community diversity and structure were studied by sequencing of 16S rRNA gene clone libraries. MBC and enzyme activities were not affected by high Ni contents. Changes in SMF were more related to the organic matter content of soils (SOM) than to their available Ni. Phylogeny-based methods detected qualitative and quantitative differences in pairwise comparisons of bacterial community structures of the three sites. However, no correlations between community structure differences and SOM or SMF were detected. We believe this work presents benchmark information on SMF, diversity, and structure of bacterial communities for a unique type of environment within the Cerrado biome.
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13
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Daae FL, Økland I, Dahle H, Jørgensen SL, Thorseth IH, Pedersen RB. Microbial life associated with low-temperature alteration of ultramafic rocks in the Leka ophiolite complex. GEOBIOLOGY 2013; 11:318-339. [PMID: 23551703 DOI: 10.1111/gbi.12035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 03/15/2013] [Indexed: 06/02/2023]
Abstract
Water-rock interactions in ultramafic lithosphere generate reduced chemical species such as hydrogen that can fuel subsurface microbial communities. Sampling of this environment is expensive and technically demanding. However, highly accessible, uplifted oceanic lithospheres emplaced onto continental margins (ophiolites) are potential model systems for studies of the subsurface biosphere in ultramafic rocks. Here, we describe a microbiological investigation of partially serpentinized dunite from the Leka ophiolite (Norway). We analysed samples of mineral coatings on subsurface fracture surfaces from different depths (10-160 cm) and groundwater from a 50-m-deep borehole that penetrates several major fracture zones in the rock. The samples are suggested to represent subsurface habitats ranging from highly anaerobic to aerobic conditions. Water from a surface pond was analysed for comparison. To explore the microbial diversity and to make assessments about potential metabolisms, the samples were analysed by microscopy, construction of small subunit ribosomal RNA gene clone libraries, culturing and quantitative-PCR. Different microbial communities were observed in the groundwater, the fracture-coating material and the surface water, indicating that distinct microbial ecosystems exist in the rock. Close relatives of hydrogen-oxidizing Hydrogenophaga dominated (30% of the bacterial clones) in the oxic groundwater, indicating that microbial communities in ultramafic rocks at Leka could partially be driven by H2 produced by low-temperature water-rock reactions. Heterotrophic organisms, including close relatives of hydrocarbon degraders possibly feeding on products from Fischer-Tropsch-type reactions, dominated in the fracture-coating material. Putative hydrogen-, ammonia-, manganese- and iron-oxidizers were also detected in fracture coatings and the groundwater. The microbial communities reflect the existence of different subsurface redox conditions generated by differences in fracture size and distribution, and mixing of fluids. The particularly dense microbial communities in the shallow fracture coatings seem to be fuelled by both photosynthesis and oxidation of reduced chemical species produced by water-rock reactions.
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Affiliation(s)
- F L Daae
- Department of Biology, Centre for Geobiology, Bergen, Norway.
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Jin Q, Han H, Hu X, Li X, Zhu C, Ho SYW, Ward RD, Zhang AB. Quantifying species diversity with a DNA barcoding-based method: Tibetan moth species (Noctuidae) on the Qinghai-Tibetan Plateau. PLoS One 2013; 8:e64428. [PMID: 23741330 PMCID: PMC3669328 DOI: 10.1371/journal.pone.0064428] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 04/14/2013] [Indexed: 12/18/2022] Open
Abstract
With the ongoing loss of biodiversity, there is a great need for fast and effective ways to assess species richness and diversity: DNA barcoding provides a powerful new tool for this. We investigated this approach by focusing on the Tibetan plateau, which is one of the world's top biodiversity hotspots. There have been few studies of its invertebrates, although they constitute the vast majority of the region's diversity. Here we investigated species diversity of the lepidopteran family Noctuidae, across different environmental gradients, using measurements based on traditional morphology as well as on DNA barcoding. The COI barcode showed an average interspecific K2P distance of 9.45±2.08%, which is about four times larger than the mean intraspecific distance (1.85±3.20%). Using six diversity indices, we did not detect any significant differences in estimated species diversity between measurements based on traditional morphology and on DNA barcoding. Furthermore, we found strong positive correlations between them, indicating that barcode-based measures of species diversity can serve as a good surrogate for morphology-based measures in most situations tested. Eastern communities were found to have significantly higher diversity than Western ones. Among 22 environmental factors tested, we found that three (precipitation of driest month, precipitation of driest quarter, and precipitation of coldest quarter) were significantly correlated with species diversity. Our results indicate that these factors could be the key ecological factors influencing the species diversity of the lepidopteran family Noctuidae on the Tibetan plateau.
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Affiliation(s)
- Qian Jin
- College of Life Sciences, Capital Normal University, Beijing, People's Republic of China
| | - Huilin Han
- School of Forestry, Experiment Center, Northeast Forestry University, Haerbin, People's Republic of China
| | - XiMin Hu
- College of Life Sciences, Capital Normal University, Beijing, People's Republic of China
| | - XinHai Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - ChaoDong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Simon Y. W. Ho
- School of Biological Sciences, University Of Sydney, Sydney, Australia
| | - Robert D. Ward
- Wealth from Oceans Flagship, CSIRO Marine and Atmospheric Research, Hobart, Tasmania, Australia
| | - Ai-bing Zhang
- College of Life Sciences, Capital Normal University, Beijing, People's Republic of China
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15
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Porter SS, Rice KJ. TRADE-OFFS, SPATIAL HETEROGENEITY, AND THE MAINTENANCE OF MICROBIAL DIVERSITY. Evolution 2012; 67:599-608. [DOI: 10.1111/j.1558-5646.2012.01788.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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16
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Daghino S, Murat C, Sizzano E, Girlanda M, Perotto S. Fungal diversity is not determined by mineral and chemical differences in serpentine substrates. PLoS One 2012; 7:e44233. [PMID: 23028507 PMCID: PMC3447857 DOI: 10.1371/journal.pone.0044233] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 07/30/2012] [Indexed: 12/03/2022] Open
Abstract
The physico-chemical properties of serpentine soils lead to strong selection of plant species. Whereas many studies have described the serpentine flora, little information is available on the fungal communities dwelling in these sites. Asbestos minerals, often associated with serpentine rocks, can be weathered by serpentine-isolated fungi, suggesting an adaptation to this substrate. In this study, we have investigated whether serpentine substrates characterized by the presence of rocks with distinct mineral composition could select for different fungal communities. Both fungal isolation and 454 pyrosequencing of amplicons obtained from serpentine samples following direct DNA extraction revealed some fungal taxa shared by the four ophiolitic substrates, but also highlighted several substrate-specific taxa. Bootstrap analysis of 454 OTU abundances indicated weak clustering of fungal assemblages from the different substrates, which did not match substrate classification based on exchangeable macronutrients and metals. Intra-substrate variability, as assessed by DGGE profiles, was similar across the four serpentine substrates, and comparable to inter-substrate variability. These findings indicate the absence of a correlation between the substrate (mineral composition and available cations) and the diversity of the fungal community. Comparison of culture-based and culture-independent methods supports the higher taxonomic precision of the former, as complementation of the better performance of the latter.
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Affiliation(s)
- Stefania Daghino
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy.
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17
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Magalhães C, Stevens MI, Cary SC, Ball BA, Storey BC, Wall DH, Türk R, Ruprecht U. At limits of life: multidisciplinary insights reveal environmental constraints on biotic diversity in continental Antarctica. PLoS One 2012; 7:e44578. [PMID: 23028563 PMCID: PMC3446939 DOI: 10.1371/journal.pone.0044578] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 08/09/2012] [Indexed: 11/30/2022] Open
Abstract
Multitrophic communities that maintain the functionality of the extreme Antarctic terrestrial ecosystems, while the simplest of any natural community, are still challenging our knowledge about the limits to life on earth. In this study, we describe and interpret the linkage between the diversity of different trophic level communities to the geological morphology and soil geochemistry in the remote Transantarctic Mountains (Darwin Mountains, 80°S). We examined the distribution and diversity of biota (bacteria, cyanobacteria, lichens, algae, invertebrates) with respect to elevation, age of glacial drift sheets, and soil physicochemistry. Results showed an abiotic spatial gradient with respect to the diversity of the organisms across different trophic levels. More complex communities, in terms of trophic level diversity, were related to the weakly developed younger drifts (Hatherton and Britannia) with higher soil C/N ratio and lower total soluble salts content (thus lower conductivity). Our results indicate that an increase of ion concentration from younger to older drift regions drives a succession of complex to more simple communities, in terms of number of trophic levels and diversity within each group of organisms analysed. This study revealed that integrating diversity across multi-trophic levels of biotic communities with abiotic spatial heterogeneity and geological history is fundamental to understand environmental constraints influencing biological distribution in Antarctic soil ecosystems.
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Affiliation(s)
- Catarina Magalhães
- Centre of Marine and Environmental Research, University of Porto, Portugal, Rua dos Bragas, Porto, Portugal.
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18
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Larouche JR, Bowden WB, Giordano R, Flinn MB, Crump BC. Microbial biogeography of arctic streams: exploring influences of lithology and habitat. Front Microbiol 2012; 3:309. [PMID: 22936932 PMCID: PMC3426929 DOI: 10.3389/fmicb.2012.00309] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 08/03/2012] [Indexed: 01/18/2023] Open
Abstract
Terminal restriction fragment length polymorphism and 16S rRNA gene sequencing were used to explore the community composition of bacterial communities in biofilms on sediments (epipssamon) and rocks (epilithon) in stream reaches that drain watersheds with contrasting lithologies in the Noatak National Preserve, Alaska. Bacterial community composition varied primarily by stream habitat and secondarily by lithology. Positive correlations were detected between bacterial community structure and nutrients, base cations, and dissolved organic carbon. Our results showed significant differences at the stream habitat, between epipssamon and epilithon bacterial communities, which we expected. Our results also showed significant differences at the landscape scale that could be related to different lithologies and associated stream biogeochemistry. These results provide insight into the bacterial community composition of little known and pristine arctic stream ecosystems and illustrate how differences in the lithology, soils, and vegetation community of the terrestrial environment interact to influence stream bacterial taxonomic richness and composition.
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Affiliation(s)
- Julia R. Larouche
- Rubenstein School of Environment and Natural Resources, University of VermontBurlington, VT, USA
| | - William B. Bowden
- Rubenstein School of Environment and Natural Resources, University of VermontBurlington, VT, USA
| | - Rosanna Giordano
- Institute of Natural Resource Sustainability, Illinois Natural History Survey, University of Illinois at Urbana–ChampaignIL, USA
| | | | - Byron C. Crump
- Horn Point Laboratory, Center for Environmental Science, University of MarylandCambridge, MD, USA
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García-Salamanca A, Molina-Henares MA, van Dillewijn P, Solano J, Pizarro-Tobías P, Roca A, Duque E, Ramos JL. Bacterial diversity in the rhizosphere of maize and the surrounding carbonate-rich bulk soil. Microb Biotechnol 2012; 6:36-44. [PMID: 22883414 PMCID: PMC3815383 DOI: 10.1111/j.1751-7915.2012.00358.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 07/02/2012] [Accepted: 07/10/2012] [Indexed: 11/28/2022] Open
Abstract
Maize represents one of the main cultivar for food and energy and crop yields are influenced by soil physicochemical and climatic conditions. To study how maize plants influence soil microbes we have examined microbial communities that colonize maize plants grown in carbonate-rich soil (pH 8.5) using culture-independent, PCR-based methods. We observed a low proportion of unclassified bacteria in this soil whether it was planted or unplanted. Our results indicate that a higher complexity of the bacterial community is present in bulk soil with microbes from nine phyla, while in the rhizosphere microbes from only six phyla were found. The predominant microbes in bulk soil were bacteria of the phyla Acidobacteria, Bacteroidetes and Proteobacteria, while Gammaproteobacteria of the genera Pseudomonas and Lysobacter were the predominant in the rhizosphere. As Gammaproteobacteria respond chemotactically to exudates and are efficient in the utilization of plants exudate products, microbial communities associated to the rhizosphere seem to be plant-driven. It should be noted that Gammaproteobacteria made available inorganic nutrients to the plants favouring plant growth and then the benefit of the interaction is common.
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Affiliation(s)
- Adela García-Salamanca
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008, Granada, Spain
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20
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Yarwood SA, Bottomley PJ, Myrold DD. Soil microbial communities associated with Douglas-fir and red alder stands at high- and low-productivity forest sites in Oregon, USA. MICROBIAL ECOLOGY 2010; 60:606-617. [PMID: 20449582 DOI: 10.1007/s00248-010-9675-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 04/10/2010] [Indexed: 05/29/2023]
Abstract
Communities of archaea, bacteria, and fungi were examined in forest soils located in the Oregon Coast Range and the inland Cascade Mountains. Soils from replicated plots of Douglas-fir (Pseudotsuga menziesii) and red alder (Alnus rubra) were characterized using fungal ITS (internal transcribed spacer region), eubacterial 16S rRNA, and archaeal 16S rRNA primers. Population size was measured with quantitative (Q)-PCR and composition was examined using length heterogeneity (LH)-PCR for fungal composition, terminal restriction fragment length (T-RFLP) profiles for bacterial and archaeal composition, and sequencing to identify dominant community members. Whereas fungal and archaeal composition varied between sites and dominant tree species, bacterial communities only varied between sites. The abundance of archaeal gene copy numbers was found to be greater in coastal compared to montane soils accounting for 11% of the prokaryotic community. Crenarchaea groups 1.1a-associated, 1.1b, 1.1c, and 1.1c-associated were putatively identified. A greater abundance of Crenarchaea 1.1b indicator fragments was found in acidic (pH 4) soils with low C:N ratios under red alder. In coastal soils, 25% of fungal sequences were putatively identified as basidiomycetous yeasts belonging to the genus Cryptococcus. Although the function of these yeasts in soil is not known, they could significantly contribute to decomposition processes in coastal soils distinguished by rapid tree growth, high N content, low pH, and frequent water-saturation events.
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Affiliation(s)
- Stephanie A Yarwood
- Department of Microbiology, Oregon State University, Nash Hall 220, Corvallis, OR 97331, USA.
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21
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Uroz S, Buée M, Murat C, Frey-Klett P, Martin F. Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2010; 2:281-8. [PMID: 23766079 DOI: 10.1111/j.1758-2229.2009.00117.x] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Several reports have highlighted that forest soil samples are more phylum-rich than agricultural soil samples. However, little is known about the structure and richness of the bacterial communities in forest soil. Using high-throughput next generation 454 pyrosequencing, we deeply investigated the diversity of bacterial communities colonizing the oak rhizosphere niche and the surrounding soil. From three spatially independent soil samples, we obtained over 300 000 partial 16S rRNA gene sequences. The most abundant bacterial groups were the Acidobacteria, Proteobacteria and unclassified bacteria. Multifactorial analysis of the relative proportions of the different phyla revealed a net differentiation of the bacterial communities present in the rhizosphere and soil environments, suggesting an oak rhizosphere effect. Significantly more β-, γ- and unclassified Proteobacteria inhabited the rhizosphere when compared with the surrounding soil. Conversely, significantly more unclassified bacteria were detected in the bulk soil than in the rhizosphere, demonstrating that the soil remains a challenging reservoir of complexity. This work increases our understanding of the niche effect on bacterial diversity and on the rare phylogenetic groups inhabiting the soil.
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Affiliation(s)
- Stéphane Uroz
- INRA, UMR1136 INRA-Nancy Université'Interactions Arbres-Microorganismes', IFR 110, Centre INRA de Nancy, 54280 Champenoux, France
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Taketani RG, Franco NO, Rosado AS, van Elsas JD. Microbial community response to a simulated hydrocarbon spill in mangrove sediments. J Microbiol 2010; 48:7-15. [PMID: 20221723 DOI: 10.1007/s12275-009-0147-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 08/09/2009] [Indexed: 02/01/2023]
Abstract
In this study, we examined the hypothesis that the microbial communities in mangrove sediments with different chemical and historical characteristics respond differently to the disturbance of a hydrocarbon spill. Two different mangrove sediments were sampled, one close to an oil refinery that had suffered a recent oil spill and another that had not been in contact with oil. Based on the sampled sediment, two sets of mesocosms were built, and oil was added to one of them. They were subjected to mimicked mangrove conditions and monitored for 75 days. Archaeal and bacterial communities were evaluated through PCR-DGGE. Both communities showed the emergence of small numbers of novel bands in response to oil pollution. 16S rRNA gene clone libraries were constructed from both mesocosms before the addition of oil and at day 75 after oil addition. LIBSHUFF analysis showed that both mangrove-based mesocosms contained similar communities at the start of the experiment and that they were different from the initial one, as well as from each other, after 75 days. These results hint at a role of environmental history that is not obvious from community diversity indicators, but is apparent from the response to the applied stress.
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Affiliation(s)
- Rodrigo Gouvêa Taketani
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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23
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Lin YT, Huang YJ, Tang SL, Whitman WB, Coleman DC, Chiu CY. Bacterial community diversity in undisturbed perhumid montane forest soils in Taiwan. MICROBIAL ECOLOGY 2010; 59:369-78. [PMID: 19727930 DOI: 10.1007/s00248-009-9574-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 08/01/2009] [Indexed: 05/15/2023]
Abstract
The diversity and composition of soil bacterial communities in three topographic sites (summit, foot slope, and lakeshore) from subtropical montane forest ecosystem in Taiwan were examined by using 16S rRNA gene clone library analysis. This locality is temperate, perhumid, and has low soil acidity (pH < 4), which is an uncommon ecosystem in a monsoonal part of Southeast Asia. A total of 481 clones were sequenced and placed into ten phylogenetic groups according to their similarities to type strains of described organisms. Toposequence of the transect was investigated from summit to foot slope and at the lakeshore. More than 86% of the clones were affiliated with members of the Proteobacteria, Acidobacteria, and Actinobacteria. Within the Proteobacteria, the beta-Proteobacteria was the most abundant, then alpha-Proteobacteria and gamma-Proteobacteria. Based on the Shannon diversity index (H) analysis, the bacterial community in the foot slope was the most diverse (H = 0.86) and that in summit was the least diverse (H = 0.68). The composition and diversity of soil bacterial communities in the three sites suggested no trend with topographic change. Less than 20% of the sequences were Acidobacteria-affiliated clones. The low proportion of Acidobacteria observed may be related to the high soil moisture and anaerobic microhabitats. Moreover, Shannon diversity indices revealed these bacterial communities to have lower diversity than that of other temperate (H = 0.90) and tropical forest (H = 0.82) ecosystems. The extreme acidity of soil pH and high soil moisture of this forest may explain composition and reduced the diversity of these soil bacterial communities.
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Affiliation(s)
- Yu-Te Lin
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
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Rajkumar M, Vara Prasad MN, Freitas H, Ae N. Biotechnological applications of serpentine soil bacteria for phytoremediation of trace metals. Crit Rev Biotechnol 2009; 29:120-30. [PMID: 19514893 DOI: 10.1080/07388550902913772] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Serpentine or ultramafic soils are produced by weathering and pedogenesis of ultramafic rocks that are characterized by high levels of Ni, Cr, and sometimes Co, but contain low levels of essential nutrients such as N, P, K, and Ca. A number of plant species endemic to serpentine soils are capable of accumulating exceptionally high concentrations of Ni, Zn, and Co. These plants are known as metal "hyperaccumulators." The function of hyperaccumulation depends not only on the plant, but also on the interaction of the plant roots with rhizosphere microbes and the concentrations of bioavailable metals in the soil. The rhizosphere provides a complex and dynamic microenvironment where microorganisms, in association with roots, form unique communities that have considerable potential for the detoxification of hazardous materials. The rhizosphere bacteria play a significant role on plant growth in serpentine soils by various mechanisms, namely, fixation of atmospheric nitrogen, utilization of 1-aminocyclopropane-1-carboxylic acid (ACC) as the sole N source, production of siderophores, or production of plant growth regulators (hormones). Further, many microorganisms in serpentine soil are able to solubilize "unavailable" forms of heavy metal-bearing minerals by excreting organic acids. In addition, the metal-resistant serpentine isolates increase the efficiency of phytoextraction directly by enhancing the metal accumulation in plant tissues and indirectly by promoting the shoot and root biomass of hyperaccumulators. Hence, isolation of the indigenous and stress-adapted beneficial bacteria serve as a potential biotechnological tool for inoculation of plants for the successful restoration of metal-contaminated ecosystems. In this study, we highlight the diversity and beneficial features of serpentine bacteria and discuss their potential in phytoremediation of serpentine and anthropogenically metal-contaminated soils.
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Affiliation(s)
- Mani Rajkumar
- Centre for Functional Ecology, Department of Botany, University of Coimbra, Portugal.
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25
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Boyd RS, Kruckeberg AR, Rajakaruna N. Biology of Ultramafic Rocks and Soils: Research Goals for the Future. Northeast Nat (Steuben) 2009. [DOI: 10.1656/045.016.0530] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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D'Amico ME, Calabrese F, Rossetti A, Previtali F. Heavy Metals and Biological Properties of Subalpine Soils on Ophiolites in the Italian Western Alps. Northeast Nat (Steuben) 2009. [DOI: 10.1656/045.016.0516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Daghino S, Turci F, Tomatis M, Girlanda M, Fubini B, Perotto S. Weathering of chrysotile asbestos by the serpentine rock-inhabiting fungus Verticillium leptobactrum. FEMS Microbiol Ecol 2009; 69:132-41. [PMID: 19453742 DOI: 10.1111/j.1574-6941.2009.00695.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Verticillium leptobactrum, a rare fungal species, has repeatedly been isolated from serpentinic rocks in the Western Alps, thus suggesting that it adapts easily to this selective mineral substrate. The rRNA internal transcribed spacer region of several isolates has been sequenced to confirm their identity and taxonomic position within Verticillium, a recently revised polyphyletic entity. Isolates of V. leptobactrum have also been investigated to establish their ability to weather asbestos chrysotile, the most common mineral in the isolation sites. The results of solubilization assays on magnesium and silicon, as well as measurement of the Mg/Si ratio in the asbestos fibres after exposure to fungal mycelia, indicate a high bioweathering activity of V. leptobactrum towards chrysotile. Comparison with data on Fusarium oxysporum shows differences among species, with V. leptobactrum being more active than F. oxysporum in removing structural ions from chrysotile. Asbestos weathering by fungi could be envisaged as a bioremediation strategy for hazardous asbestos-rich soils (e.g. abandoned mines). Fungi that have adapted to live in serpentine sites could be good candidates for this purpose.
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Affiliation(s)
- Stefania Daghino
- Interdepartmental Centre G. Scansetti for Studies on Asbestos and Other Toxic Particulates, University of Torino, 10125 Turin, Italy
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Valentini A, Pompanon F, Taberlet P. DNA barcoding for ecologists. Trends Ecol Evol 2008; 24:110-7. [PMID: 19100655 DOI: 10.1016/j.tree.2008.09.011] [Citation(s) in RCA: 511] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Revised: 08/26/2008] [Accepted: 09/08/2008] [Indexed: 12/14/2022]
Abstract
DNA barcoding - taxon identification using a standardized DNA region - has received much attention recently, and is being further developed through an international initiative. We anticipate that DNA barcoding techniques will be increasingly used by ecologists. They will be able to not only identify a single species from a specimen or an organism's remains but also determine the species composition of environmental samples. Short DNA fragments persist in the environment and might allow an assessment of local biodiversity from soil or water. Even DNA-based diet composition can be estimated using fecal samples. Here we review the new avenues offered to ecologists by DNA barcoding, particularly in the context of new sequencing technologies.
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Affiliation(s)
- Alice Valentini
- Laboratoire d'Ecologie Alpine, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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29
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Casper BB, Bentivenga SP, Ji B, Doherty JH, Edenborn HM, Gustafson DJ. PLANT–SOIL FEEDBACK: TESTING THE GENERALITY WITH THE SAME GRASSES IN SERPENTINE AND PRAIRIE SOILS. Ecology 2008; 89:2154-64. [DOI: 10.1890/07-1277.1] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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30
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Stott MB, Crowe MA, Mountain BW, Smirnova AV, Hou S, Alam M, Dunfield PF. Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand. Environ Microbiol 2008; 10:2030-41. [DOI: 10.1111/j.1462-2920.2008.01621.x] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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Klocke M, Nettmann E, Bergmann I, Mundt K, Souidi K, Mumme J, Linke B. Characterization of the methanogenic Archaea within two-phase biogas reactor systems operated with plant biomass. Syst Appl Microbiol 2008; 31:190-205. [DOI: 10.1016/j.syapm.2008.02.003] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2007] [Revised: 02/13/2008] [Accepted: 02/26/2008] [Indexed: 10/22/2022]
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Abstract
Diversity measurement is important for understanding community structure and dynamics, but has been particularly challenging for microorganisms. Microbial community characterization using small subunit rRNA (SSU rRNA) gene sequences has revealed an extensive, previously unsuspected diversity that we are only now beginning to understand, especially now that advanced sequencing technologies are producing datasets containing hundreds of thousands of sequences from hundreds of samples. Efforts to quantify microbial diversity often use taxon-based methods that ignore the fact that not all species are equally related, which can therefore obscure important patterns in the data. For example, alpha-diversity (diversity within communities) is often estimated as the number of species in a community (species richness), and beta-diversity (partitioning of diversity among communities) is often based on the number of shared species. Methods for measuring alpha- and beta-diversity that account for different levels of divergence between individuals have recently been more widely applied. These methods are more powerful than taxon-based methods because microorganisms in a community differ dramatically in sequence similarity, which also often correlates with phenotypic similarity in key features such as metabolic capabilities. Consequently, divergence-based methods are providing new insights into microbial community structure and function.
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Affiliation(s)
- Catherine A Lozupone
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309-0215, USA.
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33
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Abstract
The bacterial phylogenetic structure of soils from four distinctly different sites in South and North America was analyzed. One hundred and thirty-nine thousand sequences of the V9 region of the small subunit of the bacterial ribosomal RNA gene generated for a previous study were used for this work. Whereas the previous work estimated levels of species richness, this study details the degree of bacterial community overlap between the four soils. Sequences from the four soils were classified and grouped into different phyla and then assigned to operational taxonomic units (OTUs) as defined by 97 or 100% sequence similarity. Pairwise Jaccard and theta similarity indices averaged over all phyla equalled 6 and 12% respectively at the 97% similarity level, and 15% for both at the 100% similarity level. At 100 and 97% sequence similarity, 1.5 and 4.1% of OTUs were found in all four soils respectively, and 87.9 and 74.4%, respectively were a unique particular soil. These analyses, based on the largest soil bacterial sequence retrieval to date, establish the high degree of community structure difference for randomly sampled dissimilar soils and support the idea that wide sampling is important for bioprospecting. The 10 most abundant cultured genera were determined in each soil. These 10 genera comprised a significant proportion of the reads obtained from each soil (31.3-37.4%). Chitinophaga was the most abundant or the second most abundant genus in all four soils with 7.5-13.8% of the total bacterial sequences in these soils. The striking result is that several culturable genera, whose roles in soil are virtually unknown, were found among these dominant sequences.
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Niederberger TD, McDonald IR, Hacker AL, Soo RM, Barrett JE, Wall DH, Cary SC. Microbial community composition in soils of Northern Victoria Land, Antarctica. Environ Microbiol 2008; 10:1713-24. [PMID: 18373679 DOI: 10.1111/j.1462-2920.2008.01593.x] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Biotic communities and ecosystem dynamics in terrestrial Antarctica are limited by an array of extreme conditions including low temperatures, moisture and organic matter availability, high salinity, and a paucity of biodiversity to facilitate key ecological processes. Recent studies have discovered that the prokaryotic communities in these extreme systems are highly diverse with patchy distributions. Investigating the physical and biological controls over the distribution and activity of microbial biodiversity in Victoria Land is essential to understanding ecological functioning in this region. Currently, little information on the distribution, structure and activity of soil communities anywhere in Victoria Land are available, and their sensitivity to potential climate change remains largely unknown. We investigated soil microbial communities from low- and high-productivity habitats in an isolated Antarctic location to determine how the soil environment impacts microbial community composition and structure. The microbial communities in Luther Vale, Northern Victoria Land were analysed using bacterial 16S rRNA gene clone libraries and were related to soil geochemical parameters and classical morphological analysis of soil metazoan invertebrate communities. A total of 323 16S rRNA gene sequences analysed from four soils spanning a productivity gradient indicated a high diversity (Shannon-Weaver values > 3) of phylotypes within the clone libraries and distinct differences in community structure between the two soil productivity habitats linked to water and nutrient availability. In particular, members of the Deinococcus/Thermus lineage were found exclusively in the drier, low-productivity soils, while Gammaproteobacteria of the genus Xanthomonas were found exclusively in high-productivity soils. However, rarefaction curves indicated that these microbial habitats remain under-sampled. Our results add to the recent literature suggesting that there is a higher biodiversity within Antarctic soils than previously expected.
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