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Rodríguez-Valdecantos G, Torres-Rojas F, Muñoz-Echeverría S, del Rocío Mora-Ruiz M, Rosselló-Móra R, Cid-Cid L, Ledger T, González B. Aromatic compounds depurative and plant growth promotion rhizobacteria abilities of Allenrolfea vaginata ( Amaranthaceae) rhizosphere microbial communities from a solar saltern hypersaline soil. Front Microbiol 2023; 14:1251602. [PMID: 37954249 PMCID: PMC10635022 DOI: 10.3389/fmicb.2023.1251602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/09/2023] [Indexed: 11/14/2023] Open
Abstract
Introduction This work investigates whether rhizosphere microorganisms that colonize halophyte plants thriving in saline habitats can tolerate salinity and provide beneficial effects to their hosts, protecting them from environmental stresses, such as aromatic compound (AC) pollution. Methods To address this question, we conducted a series of experiments. First, we evaluated the effects of phenol, tyrosine, 4-hydroxybenzoic acid, and 2,4-dichlorophenoxyacetic (2,4-D) acids on the soil rhizosphere microbial community associated with the halophyte Allenrolfea vaginata. We then determined the ability of bacterial isolates from these microbial communities to utilize these ACs as carbon sources. Finally, we assessed their ability to promote plant growth under saline conditions. Results Our study revealed that each AC had a different impact on the structure and alpha and beta diversity of the halophyte bacterial (but not archaeal) communities. Notably, 2,4-D and phenol, to a lesser degree, had the most substantial decreasing effects. The removal of ACs by the rhizosphere community varied from 15% (2,4-D) to 100% (the other three ACs), depending on the concentration. Halomonas isolates were the most abundant and diverse strains capable of degrading the ACs, with strains of Marinobacter, Alkalihalobacillus, Thalassobacillus, Oceanobacillus, and the archaea Haladaptatus also exhibiting catabolic properties. Moreover, our study found that halophile strains Halomonas sp. LV-8T and Marinobacter sp. LV-48T enhanced the growth and protection of Arabidopsis thaliana plants by 30% to 55% under salt-stress conditions. Discussion These results suggest that moderate halophile microbial communities may protect halophytes from salinity and potential adverse effects of aromatic compounds through depurative processes.
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Affiliation(s)
- Gustavo Rodríguez-Valdecantos
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Felipe Torres-Rojas
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Sofía Muñoz-Echeverría
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Merit del Rocío Mora-Ruiz
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Esporles, Spain
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Esporles, Spain
| | - Luis Cid-Cid
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Thomas Ledger
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Bernardo González
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
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Rozaliyani A, Abdullah A, Setianingrum F, Sjamsuridzal W, Wahyuningsih R, Bowolaksono A, Fatril AE, Adawiyah R, Tugiran M, Syam R, Wibowo H, Kosmidis C, Denning DW. Unravelling the Molecular Identification and Antifungal Susceptibility Profiles of Aspergillus spp. Isolated from Chronic Pulmonary Aspergillosis Patients in Jakarta, Indonesia: The Emergence of Cryptic Species. J Fungi (Basel) 2022; 8:jof8040411. [PMID: 35448642 PMCID: PMC9024953 DOI: 10.3390/jof8040411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/16/2022] Open
Abstract
Cryptic species of Aspergillus have rapidly increased in the last few decades. Chronic pulmonary aspergillosis (CPA) is a debilitating fungal infection frequently affecting patients with previous TB. The identification and antifungal susceptibility profiles of different species of Aspergillus are important to support the management of CPA. The aim of this study was to describe the molecular and susceptibility profiles of Aspergillus isolated from CPA patients. The species identity of isolates was determined by combined DNA analyses of internal transcribed space (ITS), partial β-tubulin genes, and part of the calmodulin gene. We revealed a high (27%) prevalence of cryptic species among previous tuberculosis patients with persistent symptoms. Twenty-nine (49%) patients met the criteria for diagnosis of CPA with 24% containing Aspergillus cryptic species. This is the first report of five cryptic Aspergillus species from clinical isolates in Indonesia: A. aculea tus, A. neoniger, A. brunneoviolacues, A. welwitschiae, and A. tubingensis. Significantly, there was decreased sensitivity against itraconazole in the CPA group (66% susceptible to itraconazole) compared to the non-CPA group (90% susceptible to itraconazole) (p = 0.003). The species-level characterisation of Aspergillus and its antifungal susceptibility tests demands greater attention to better the management of CPA patients.
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Affiliation(s)
- Anna Rozaliyani
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia; (F.S.); (R.W.); (A.E.F.); (R.A.); (M.T.); (R.S.); (H.W.)
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
- Correspondence: ; Tel.: +62-21-3102135; Fax: +62-21-3983201
| | - Asriyani Abdullah
- Magister Program of Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia;
| | - Findra Setianingrum
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia; (F.S.); (R.W.); (A.E.F.); (R.A.); (M.T.); (R.S.); (H.W.)
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Wellyzar Sjamsuridzal
- Department of Biology, Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Indonesia, Depok 16424, Indonesia; (W.S.); (A.B.)
| | - Retno Wahyuningsih
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia; (F.S.); (R.W.); (A.E.F.); (R.A.); (M.T.); (R.S.); (H.W.)
- Department of Parasitology, Faculty of Medicine, Universitas Kristen, Jakarta 13530, Indonesia
| | - Anom Bowolaksono
- Department of Biology, Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Indonesia, Depok 16424, Indonesia; (W.S.); (A.B.)
| | - Ayu Eka Fatril
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia; (F.S.); (R.W.); (A.E.F.); (R.A.); (M.T.); (R.S.); (H.W.)
| | - Robiatul Adawiyah
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia; (F.S.); (R.W.); (A.E.F.); (R.A.); (M.T.); (R.S.); (H.W.)
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Mulyati Tugiran
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia; (F.S.); (R.W.); (A.E.F.); (R.A.); (M.T.); (R.S.); (H.W.)
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Ridhawati Syam
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia; (F.S.); (R.W.); (A.E.F.); (R.A.); (M.T.); (R.S.); (H.W.)
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Heri Wibowo
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia; (F.S.); (R.W.); (A.E.F.); (R.A.); (M.T.); (R.S.); (H.W.)
- Magister Program of Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia;
| | - Chris Kosmidis
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M23 9LT, UK; (C.K.); (D.W.D.)
- Manchester Academic Health Science Centre, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M23 9LT, UK
| | - David W. Denning
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M23 9LT, UK; (C.K.); (D.W.D.)
- Manchester Academic Health Science Centre, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M23 9LT, UK
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Zhang X, Liu S, Jiang Z, Wu Y, Huang X. Gradient of microbial communities around seagrass roots was mediated by sediment grain size. Ecosphere 2022. [DOI: 10.1002/ecs2.3942] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Xia Zhang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province Sanya Institute of Oceanology, SCSIO Sanya China
| | - Zhijian Jiang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
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Kour D, Kaur T, Devi R, Yadav A, Singh M, Joshi D, Singh J, Suyal DC, Kumar A, Rajput VD, Yadav AN, Singh K, Singh J, Sayyed RZ, Arora NK, Saxena AK. Beneficial microbiomes for bioremediation of diverse contaminated environments for environmental sustainability: present status and future challenges. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:24917-24939. [PMID: 33768457 DOI: 10.1007/s11356-021-13252-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 02/28/2021] [Indexed: 05/21/2023]
Abstract
Over the past few decades, the rapid development of agriculture and industries has resulted in contamination of the environment by diverse pollutants, including heavy metals, polychlorinated biphenyls, plastics, and various agrochemicals. Their presence in the environment is of great concern due to their toxicity and non-biodegradable nature. Their interaction with each other and coexistence in the environment greatly influence and threaten the ecological environment and human health. Furthermore, the presence of these pollutants affects the soil quality and fertility. Physicochemical techniques are used to remediate such environments, but they are less effective and demand high costs of operation. Bioremediation is an efficient, widespread, cost-effective, and eco-friendly cleanup tool. The use of microorganisms has received significant attention as an efficient biotechnological strategy to decontaminate the environment. Bioremediation through microorganisms appears to be an economically viable and efficient approach because it poses the lowest risk to the environment. This technique utilizes the metabolic potential of microorganisms to clean up contaminated environments. Many microbial genera have been known to be involved in bioremediation, including Alcaligenes, Arthrobacter, Aspergillus, Bacillus, Burkholderia, Mucor, Penicillium, Pseudomonas, Stenotrophomonas, Talaromyces, and Trichoderma. Archaea, including Natrialba and Haloferax, from extreme environments have also been reported as potent bioresources for biological remediation. Thus, utilizing microbes for managing environmental pollution is promising technology, and, in fact, the microbes provide a useful podium that can be used for an enhanced bioremediation model of diverse environmental pollutants.
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Affiliation(s)
- Divjot Kour
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, Sirmour, India
| | - Tanvir Kaur
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, Sirmour, India
| | - Rubee Devi
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, Sirmour, India
| | - Ashok Yadav
- Department of Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Manali Singh
- Invertis Institute of Engineering and Technology (IIET), Invertis University, Bareilly, Uttar Pradesh, India
| | - Divya Joshi
- Uttarakhand Pollution Control Board, Regional Office, Kashipur, Dehradun, Uttarakhand, India
| | - Jyoti Singh
- Department of Microbiology, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Deep Chandra Suyal
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, 173101, India
| | - Ajay Kumar
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | | | - Ajar Nath Yadav
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, Sirmour, India.
| | - Karan Singh
- Department of Chemistry, Indira Gandhi University, Haryana, 122502, Meerpur, Rewari, India
| | - Joginder Singh
- Department of Biotechnology, Lovely Professional University, Phagwara, Punjab, India
| | - Riyaz Z Sayyed
- Department of Microbiology, PSGVP Mandal's Arts, Science and Commerce College, Shahada, Maharashtra, India
| | - Naveen Kumar Arora
- Department of Environmental Science, Babasaheb Bhimrao Ambedkar University (A Central University), Rae Bareli Road, Uttar Pradesh, 226025, Lucknow, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms, Kusmaur, Mau, 275103, India
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Mącik M, Gryta A, Sas-Paszt L, Frąc M. The Status of Soil Microbiome as Affected by the Application of Phosphorus Biofertilizer: Fertilizer Enriched with Beneficial Bacterial Strains. Int J Mol Sci 2020; 21:E8003. [PMID: 33121206 PMCID: PMC7663420 DOI: 10.3390/ijms21218003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 01/05/2023] Open
Abstract
Regarding the unfavourable changes in agroecosystems resulting from the excessive application of mineral fertilizers, biopreparations containing live microorganisms are gaining increasing attention. We assumed that the application of phosphorus mineral fertilizer enriched with strains of beneficial microorganisms contribute to favourable changes in enzymatic activity and in the genetic and functional diversity of microbial populations inhabiting degraded soils. Therefore, in field experiments conditions, the effects of phosphorus fertilizer enriched with bacterial strains on the status of soil microbiome in two chemically degraded soil types (Brunic Arenosol - BA and Abruptic Luvisol - AL) were investigated. The field experiments included treatments with an optimal dose of phosphorus fertilizer (without microorganisms - FC), optimal dose of phosphorus fertilizer enriched with microorganisms including Paenibacillus polymyxa strain CHT114AB, Bacillus amyloliquefaciens strain AF75BB and Bacillus sp. strain CZP4/4 (FA100) and a dose of phosphorus fertilizer reduced by 40% and enriched with the above-mentioned bacteria (FA60). The analyzes performed included: the determination of the activity of the soil enzymes (protease, urease, acid phosphomonoesterase, β-glucosidase), the assessment of the functional diversity of microorganisms with the application of BIOLOGTM plates and the characterization of the genetic diversity of bacteria, archaea and fungi with multiplex terminal restriction fragment length polymorphism and next generation sequencing. The obtained results indicated that the application of phosphorus fertilizer enriched with microorganisms improved enzymatic activity, and the genetic and functional diversity of the soil microbial communities, however these effects were dependent on the soil type.
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Affiliation(s)
- Mateusz Mącik
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; (M.M.); (A.G.)
| | - Agata Gryta
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; (M.M.); (A.G.)
| | - Lidia Sas-Paszt
- Institute of Horticulture in Skierniewice, Pomologiczna 18, 96-100 Skierniewice, Poland;
| | - Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; (M.M.); (A.G.)
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Gryta A, Frąc M. Methodological Aspects of Multiplex Terminal Restriction Fragment Length Polymorphism-Technique to Describe the Genetic Diversity of Soil Bacteria, Archaea and Fungi. SENSORS 2020; 20:s20113292. [PMID: 32527006 PMCID: PMC7309186 DOI: 10.3390/s20113292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/05/2020] [Accepted: 06/07/2020] [Indexed: 01/24/2023]
Abstract
The molecular fingerprinting methods used to evaluate soil microbial diversity could also be used as effective biosensors for the purposes of monitoring ecological soil status. The biodiversity of microorganisms is a relevant index of soil activity and there is a necessity to develop tools to generate reliable results for an emerging approach in the field of environmental control using microbial diversity biosensors. This work reports a method under development for determining soil microbial diversity using high efficiency Multiplex PCR-Terminal Restriction Fragment Length Polymorphism (M-T-RFLP) for the simultaneous detection of bacteria, archaea and fungi. Three different primer sets were used in the reaction and the analytical conditions were optimized. Optimal analytical conditions were achieved using 0.5 µM of primer for bacteria and 1 µM for archaea and fungi, 4 ng of soil DNA template, and HaeIII restriction enzyme. Comparative tests using the proposed analytical approach and a single analysis of each microorganism group were carried out to indicate that both genetic profiles were similar. The Jaccard similarity coefficient between single and multiplexing approach ranged from 0.773 to 0.850 for bacteria and fungi, and 0.208 to 0.905 for archaea. In conclusion, the multiplexing and pooling approaches significantly reduced the costs and time required to perform the analyses, while maintaining a proper effectiveness.
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7
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Yadav AN, Singh J, Rastegari AA, Yadav N. Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications. ACTA ACUST UNITED AC 2020. [PMCID: PMC7123684 DOI: 10.1007/978-3-030-38453-1_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.
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Affiliation(s)
- Ajar Nath Yadav
- Department of Biotechnology, Eternal University, Baru Sahib, Himachal Pradesh India
| | - Joginder Singh
- Department of Microbiology, Lovely Professional University, Phagwara, Punjab India
| | | | - Neelam Yadav
- Gopi Nath PG College, Veer Bahadur Singh Purvanchal University, Ghazipur, Uttar Pradesh India
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Trivedi C, Reich PB, Maestre FT, Hu HW, Singh BK, Delgado-Baquerizo M. Plant-driven niche differentiation of ammonia-oxidizing bacteria and archaea in global drylands. THE ISME JOURNAL 2019; 13:2727-2736. [PMID: 31249390 PMCID: PMC6794256 DOI: 10.1038/s41396-019-0465-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 06/04/2019] [Accepted: 06/07/2019] [Indexed: 12/19/2022]
Abstract
Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale.
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Affiliation(s)
- Chanda Trivedi
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith South, NSW, 2751, Australia
| | - Peter B Reich
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith South, NSW, 2751, Australia
- Department of Forest Resources, University of Minnesota, St Paul, MN, 55108, USA
| | - Fernando T Maestre
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Móstoles, 28933, Spain
- Departamento de Ecología and Instituto Multidisciplinar para el Estudio del Medio "Ramon Margalef", Universidad de Alicante, Alicante, Spain
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith South, NSW, 2751, Australia.
- Global Centre for Land Based Innovation, Western Sydney University, Building L9, Locked Bag 1797, Penrith South, NSW, 2751, Australia.
| | - Manuel Delgado-Baquerizo
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith South, NSW, 2751, Australia.
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Móstoles, 28933, Spain.
- Cooperative Institute for Research in Environmental Science, University of Colorado Boulder, Boulder, CO, USA.
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Su Y, Lv JL, Yu M, Ma ZH, Xi H, Kou CL, He ZC, Shen AL. Long-term decomposed straw return positively affects the soil microbial community. J Appl Microbiol 2019; 128:138-150. [PMID: 31495045 DOI: 10.1111/jam.14435] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 07/24/2019] [Accepted: 08/21/2019] [Indexed: 01/12/2023]
Abstract
AIMS In order to understand the response of soil microbial communities to the long-term of decomposed straw return, the modifications of soil microbial community structure and composition induced by more than 10 years of fresh and decomposed straw return was investigated and the key environmental factors were analysed. METHODS AND RESULTS Phospholipid fatty acid analysis and high-through sequencing technique were applied to analyse the structure and composition of the soil microbial communities. Compared with fresh straw, returning decomposed straw increased the relative abundance of bacteria and fungi by 1·9 and 7·7% at a rate of ~3750 kg ha-1 , and increased by 23·1 and 5·7%, at a rate of ~7500 kg ha-1 respectively. The relative abundance of the bacteria related to soil nitrification increased, but the ones related to soil denitrification decreased with decomposed straw return, which led to higher total nitrogen contents in soils. Moreover, returning decomposed straw reduced pathogenic fungal populations (genus of Alternara), which had significantly positive correlation with soil electric conductivity. It indicated that the long-term of decomposed straw return might have lower risk of soil-borne disease mainly for the reasonable soil salinity. CONCLUSIONS Long-term of decomposed straw return could provide suitable nutrient and salinity for healthier development of soil microbial community, both in abundance and structure, compared with fresh straw return. SIGNIFICANCE AND IMPACT OF THE STUDY The results of the study helps to better understand how the microbial community modifications induced by decomposed straw return benefit on soil health. The obtained key factors impacting soil microbial community variations is meaningful in soil health management under conditions of straw return.
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Affiliation(s)
- Y Su
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - J L Lv
- Institute of Plant Nutrient, Environment and Resource, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - M Yu
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Z H Ma
- Institute of Plant Nutrient, Environment and Resource, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - H Xi
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - C L Kou
- Institute of Plant Nutrient, Environment and Resource, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Z C He
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - A L Shen
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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Aguiar LM, Dos Santos JB, Barroso GM, Laia MLD, Gonçalves JF, da Costa VAM, Brito LA. Influence of 2,4-D residues on the soil microbial community and growth of tree species. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2019; 22:69-77. [PMID: 31342787 DOI: 10.1080/15226514.2019.1644289] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The 2,4-D (2,4-dichlorophenoxyacetic acid) has low half-life in the soil, but it is capable of altering the soil microbial community. The objective of this study was to evaluate the influence of 2,4-D residues on the structure of the soil microbial community and the growth of tree species. The tolerance and phytoremediation potential of tree species were evaluated. The microbial analysis was performed by T-RFLP. The 2,4-D herbicide reduced the plant height of K. lathrophyton, number of leaves of C. ferrea and K. lathrophyton and root dry matter allocation for C. brasiliense, I. striata, P. heptaphyllum, and T. guianensis. Cucumis sativus intoxication on soil contaminated with 2,4-D was not significant. The structure of Fungi community in the rhizospheric soils of C. ferrea was altered. The herbicide 2,4-D increased the diversity of Fungi in rhizospheric soils of P. heptahyllum and R. grandis. Most tree species were tolerant, and the evaluation time was sufficient to remedy 2,4-D. The structures of the microbial communities Archaea, Bacteria, and Fungi were little influenced by 2,4-D. The diversity of the Archaea domain was not affected, the diversity of the Bacteria in Inga striata decreased while the fungi increased in Protium heptaphyllum and Richeria grandis with 2,4-D.
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Affiliation(s)
- Luciana Monteiro Aguiar
- Departamento de Agronomia, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Brasil
| | - José Barbosa Dos Santos
- Departamento de Agronomia, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Brasil
| | - Gabriela Madureira Barroso
- Departamento de Engenharia Florestal, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Brasil
| | - Marcelo Luiz de Laia
- Departamento de Engenharia Florestal, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Brasil
| | - Janaína Ferreira Gonçalves
- Departamento de Ciências Agrárias, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brasil
| | | | - Lílian Almeida Brito
- Departamento de Engenharia Florestal, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Brasil
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11
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Camacho-Montealegre CM, Rodrigues EM, Tótola MR. Microbial diversity and bioremediation of rhizospheric soils from Trindade Island - Brazil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 236:358-364. [PMID: 30739041 DOI: 10.1016/j.jenvman.2019.02.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 01/17/2019] [Accepted: 02/02/2019] [Indexed: 06/09/2023]
Abstract
Pristine environments may harbor complex microbial communities with metabolic potential for use in bioremediation of organic pollutants. This study aimed to evaluate crude oil biodegradation by microbial communities present in rhizospheric soils of Bulbostylis nesiotis and Cyperus atlanticus on Trindade Island and the compositional structure of these communities. After 60 days under aerobic conditions, Total Petroleum Hydrocarbon biodegradation ranged from 66 to 75%, depending on the plant species and the origin of the soil samples. There was no response of petroleum biodegradation to fertilization with N:P:K (80:160:80 mg dm-3). Soil contamination with crude oil did not necessarily reduce microbial diversity. The richness and diversity increased in contaminated soils in some specific situations. We conclude that microbial communities from pristine soils have the ability to remove hydrocarbons through biodegradation and that Bulbostylis nesiotis and Cyperus atlanticus inhabiting Trindade Island harbor rhizospheric microbial communities with potential for application in rhizoremediation.
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Affiliation(s)
- Celia Marcela Camacho-Montealegre
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Edmo Montes Rodrigues
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
| | - Marcos Rogério Tótola
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
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12
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Suleiman MK, Dixon K, Commander L, Nevill P, Quoreshi AM, Bhat NR, Manuvel AJ, Sivadasan MT. Evaluating the diversity and composition of bacterial communities associated with Vachellia pachyceras - the only existing native tree species in the Kuwait desert. Can J Microbiol 2018; 65:235-251. [PMID: 30495976 DOI: 10.1139/cjm-2018-0421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We investigated the diversity and composition of bacterial communities in rhizospheric and non-rhizospheric bulk soils as well as root nodule bacterial communities of Vachellia pachyceras - the only native tree species existing in the Kuwait desert. Community fingerprinting comparisons and 16S rDNA sequence identifications were used for characterization of the bacterial population using specific primers. The bacterial characterization of soil samples revealed four major phyla: Acidobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. In situ (desert) samples of both rhizospheric and non-rhizospheric bulk soil were dominated by the bacterial phyla Firmicutes and Bacteroidetes, whereas the phylum Betaproteobacteria was present only in non-rhizospheric bulk soil. Ex situ (nursery growing condition) V. pachyceras resulted in restricted bacterial communities dominated by members of a single phylum, Bacteroidetes. Results indicated that the soil organic matter and rhizospheric environments might drive the bacterial community. Despite harsh climatic conditions, data demonstrated that V. pachyceras roots harbor endophytic bacterial populations. Our findings on bacterial community composition and structure have major significance for evaluating how Kuwait's extreme climatic conditions affect bacterial communities. The baseline data obtained in this study will be useful and assist in formulating strategies in ecological restoration programs, including the application of inoculation technologies.
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Affiliation(s)
- Majda K Suleiman
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
| | - Kingsley Dixon
- b Department of Environment and Agriculture, ARC Centre for Mine Site Restoration Curtin University, Bentley, WA 6102, Australia
| | - Lucy Commander
- c School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Paul Nevill
- d Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
| | - Ali M Quoreshi
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
| | - Narayana R Bhat
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
| | - Anitha J Manuvel
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
| | - Mini T Sivadasan
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
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13
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Welz PJ, Ramond JB, Braun L, Vikram S, Le Roes-Hill M. Bacterial nitrogen fixation in sand bioreactors treating winery wastewater with a high carbon to nitrogen ratio. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 207:192-202. [PMID: 29179109 DOI: 10.1016/j.jenvman.2017.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 10/20/2017] [Accepted: 11/05/2017] [Indexed: 06/07/2023]
Abstract
Heterotrophic bacteria proliferate in organic-rich environments and systems containing sufficient essential nutrients. Nitrogen, phosphorus and potassium are the nutrients required in the highest concentrations. The ratio of carbon to nitrogen is an important consideration for wastewater bioremediation because insufficient nitrogen may result in decreased treatment efficiency. It has been shown that during the treatment of effluent from the pulp and paper industry, bacterial nitrogen fixation can supplement the nitrogen requirements of suspended growth systems. This study was conducted using physicochemical analyses and culture-dependent and -independent techniques to ascertain whether nitrogen-fixing bacteria were selected in biological sand filters used to treat synthetic winery wastewater with a high carbon to nitrogen ratio (193:1). The systems performed well, with the influent COD of 1351 mg/L being reduced by 84-89%. It was shown that the nitrogen fixing bacterial population was influenced by the presence of synthetic winery effluent in the surface layers of the biological sand filters, but not in the deeper layers. It was hypothesised that this was due to the greater availability of atmospheric nitrogen at the surface. The numbers of culture-able nitrogen-fixing bacteria, including presumptive Azotobacter spp. exhibited 1-2 log increases at the surface. The results of this study confirm that nitrogen fixation is an important mechanism to be considered during treatment of high carbon to nitrogen wastewater. If biological treatment systems can be operated to stimulate this phenomenon, it may obviate the need for nitrogen addition.
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Affiliation(s)
- Pamela J Welz
- Biocatalysis and Technical Biology Research Group, Institute for Medical and Microbial Biotechnology, Cape Peninsula University of Technology, Cape Town, South Africa.
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Lorenz Braun
- Biocatalysis and Technical Biology Research Group, Institute for Medical and Microbial Biotechnology, Cape Peninsula University of Technology, Cape Town, South Africa
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Marilize Le Roes-Hill
- Biocatalysis and Technical Biology Research Group, Institute for Medical and Microbial Biotechnology, Cape Peninsula University of Technology, Cape Town, South Africa
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Chmolowska D, Elhottová D, Krištůfek V, Kozak M, Kapustka F, Zubek S. Functioning grouped soil microbial communities according to ecosystem type, based on comparison of fallows and meadows in the same region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 599-600:981-991. [PMID: 28505890 DOI: 10.1016/j.scitotenv.2017.04.220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/18/2017] [Accepted: 04/28/2017] [Indexed: 06/07/2023]
Abstract
Predicting the composition and function of microbial communities at a bio-geographical scale, across ecosystems, is challenging. We compared six abandoned fields to six meadows to see whether soil microbial community structure and activity are more similar within the ecosystem type than between the types. We implemented bacteria and fungi phylogenetic markers profiling, phospholipids analysis, fluorescence counts of total bacteria and algae and microscopy of arbuscular mycorrhizal fungi (AMF). The functional performance of microbial communities was assessed using enzymes activity measurements as well as culturing and incubation experiments. The studied fallows and meadows had similar biomass and general structure of soil microbial communities. However, the AMF root colonization frequency was higher in the meadows than in the fallows. The AMF colonization was promoted in meadows characterised by lower availability of NO3-, P and K as well as higher soil pH, which additionally hampered plant acquisition of P at the P-limited ecosystem. Fallow and meadow microbial communities showed characteristic functional traits. Meadow soils exhibited higher basal respiration rate, while cellulose decomposition and nitrogen mineralization were faster in fallows. Even when no major differences in community structure could have been detected soil microbial communities adapted to local and/or instantaneous environmental conditions and formed functionally-specific ecotypes. This work points out the relevance of preserving meadows as reservoirs of plant diversity, which cope excellent in nutrient depleted conditions and in mountain regions thanks to microbial components of ecosystem.
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Affiliation(s)
- Dominika Chmolowska
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016, Kraków, Poland.
| | - Dana Elhottová
- Biology Centre AS CR, v.v.i., - Institute of Soil Biology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Vaclav Krištůfek
- Biology Centre AS CR, v.v.i., - Institute of Soil Biology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Maciej Kozak
- Institute of Botany, Jagiellonian University, Kopernika 27, 31-501 Kraków, Poland
| | - Filip Kapustka
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Szymon Zubek
- Institute of Botany, Jagiellonian University, Kopernika 27, 31-501 Kraków, Poland
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15
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Taxonomic and Functional Diversity of a Quercus pyrenaica Willd. Rhizospheric Microbiome in the Mediterranean Mountains. FORESTS 2017. [DOI: 10.3390/f8100390] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Rigg JL, Offord CA, Singh BK, Anderson I, Clarke S, Powell JR. Soil microbial communities influence seedling growth of a rare conifer independent of plant-soil feedback. Ecology 2016; 97:3346-3358. [DOI: 10.1002/ecy.1594] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/26/2016] [Accepted: 09/08/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Jessica L. Rigg
- Hawkesbury Institute for the Environment; Western Sydney University; Penrith New South Wales 2751 Australia
| | - Cathy A. Offord
- Australian PlantBank; Royal Botanic Gardens and Domain Trust; Australian Botanic Garden Mount Annan; Sydney New South Wales 2587 Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment; Western Sydney University; Penrith New South Wales 2751 Australia
- Global Centre for Land-Based Innovation; Western Sydney University; Penrith New South Wales 2751 Australia
| | - Ian Anderson
- Hawkesbury Institute for the Environment; Western Sydney University; Penrith New South Wales 2751 Australia
| | - Steve Clarke
- NSW Parks and Wildlife Services; Office of Environment and Heritage; Sydney New South Wales 2000 Australia
| | - Jeff R. Powell
- Hawkesbury Institute for the Environment; Western Sydney University; Penrith New South Wales 2751 Australia
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17
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Auffret MD, Karhu K, Khachane A, Dungait JAJ, Fraser F, Hopkins DW, Wookey PA, Singh BK, Freitag TE, Hartley IP, Prosser JI. The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature. PLoS One 2016; 11:e0165448. [PMID: 27798702 PMCID: PMC5087920 DOI: 10.1371/journal.pone.0165448] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 10/12/2016] [Indexed: 11/19/2022] Open
Abstract
Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited.
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Affiliation(s)
- Marc D. Auffret
- University of Aberdeen, Cruickshank Building St Machar Drive, Aberdeen AB24 3UU, United Kingdom
- * E-mail:
| | - Kristiina Karhu
- University of Exeter Amory Building, Rennes Drive, Exeter EX4 4RJ, United Kingdom
| | - Amit Khachane
- Hawkesbury Institute for the Environment, University of Western Sydney, Penrith 2751 NSW, Australia
| | - Jennifer A. J. Dungait
- Sustainable Soils and Grassland Systems Department, Rothamsted Research North Wyke, Okehampton, EX20 2SB, United Kingdom
| | - Fiona Fraser
- School of Energy, Environment and Agrifood, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, United Kingdom
| | - David W. Hopkins
- The Royal Agricultural University, Cirencester, Gloucestershire, GL7 6JS, United Kingdom
| | - Philip A. Wookey
- Institute of Life & Earth Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, United Kingdom
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment, University of Western Sydney, Penrith 2751 NSW, Australia
| | - Thomas E. Freitag
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, United Kingdom
| | - Iain P. Hartley
- University of Exeter Amory Building, Rennes Drive, Exeter EX4 4RJ, United Kingdom
| | - James I. Prosser
- University of Aberdeen, Cruickshank Building St Machar Drive, Aberdeen AB24 3UU, United Kingdom
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18
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Yamaguchi N, Baba T, Ichijo T, Himezawa Y, Enoki K, Saraya M, Li PF, Nasu M. Abundance and Community Structure of Bacteria on Asian Dust Particles Collected in Beijing, China, during the Asian Dust Season. Biol Pharm Bull 2016; 39:68-77. [PMID: 26725429 DOI: 10.1248/bpb.b15-00573] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Approximately 180 t/km(2) of Asian dust particles are estimated to fall annually on Beijing, China, and there is significant concern about the influence of microbes transported by Asian dust events on human health and downwind ecosystems. In this study, we collected Asian dust particles in Beijing, and analyzed the bacterial communities on these particles by culture-independent methods. Bacterial cells on Asian dust particles were visualized first by laser scanning microscopy, which demonstrated that Asian dust particles carry bacterial cells to Beijing. Bacterial abundance, as determined by quantitative polymerase chain reaction (PCR), was 10(8) to 10(9) cells/g, a value about 10 times higher than that in Asian dust source soils. Inter-seasonal variability of bacterial community structures among Asian dust samples, as compared by terminal restriction fragment length polymorphism (T-RFLP), was low during the Asian dust season. Several viable bacteria, including intestinal bacteria, were found in Asian dust samples by denaturing gradient gel electrophoresis (DGGE). Clone library analysis targeting 16S ribosomal RNA (rRNA) gene sequences demonstrated that bacterial phylogenetic diversity was high in the dust samples, and most of these were environmental bacteria distributed in soil and air. The dominant species in the clone library was Segetibacter aerophilus (Bacteroidetes), which was first isolated from an Asian dust sample collected in Korea. Our results also indicate the possibility of a change in the bacterial community structure during transportation and increases in desiccation-tolerant bacteria such as Firmicutes.
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19
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Rabbi SMF, Daniel H, Lockwood PV, Macdonald C, Pereg L, Tighe M, Wilson BR, Young IM. Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity. Sci Rep 2016; 6:33012. [PMID: 27615807 PMCID: PMC5018812 DOI: 10.1038/srep33012] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 08/18/2016] [Indexed: 11/23/2022] Open
Abstract
Aggregates play a key role in protecting soil organic carbon (SOC) from microbial decomposition. The objectives of this study were to investigate the influence of pore geometry on the organic carbon decomposition rate and bacterial diversity in both macro- (250–2000 μm) and micro-aggregates (53–250 μm) using field samples. Four sites of contrasting land use on Alfisols (i.e. native pasture, crop/pasture rotation, woodland) were investigated. 3D Pore geometry of the micro-aggregates and macro-aggregates were examined by X-ray computed tomography (μCT). The occluded particulate organic carbon (oPOC) of aggregates was measured by size and density fractionation methods. Micro-aggregates had 54% less μCT observed porosity but 64% more oPOC compared with macro-aggregates. In addition, the pore connectivity in micro-aggregates was lower than macro-aggregates. Despite both lower μCT observed porosity and pore connectivity in micro-aggregates, the organic carbon decomposition rate constant (Ksoc) was similar in both aggregate size ranges. Structural equation modelling showed a strong positive relationship of the concentration of oPOC with bacterial diversity in aggregates. We use these findings to propose a conceptual model that illustrates the dynamic links between substrate, bacterial diversity, and pore geometry that suggests a structural explanation for differences in bacterial diversity across aggregate sizes.
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Affiliation(s)
- S M F Rabbi
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.,Plant, Soil and Environment Systems, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - H Daniel
- Plant, Soil and Environment Systems, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - P V Lockwood
- Plant, Soil and Environment Systems, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - C Macdonald
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - L Pereg
- School of Science and Technology, University of New England, Armidale, NSW, Australia
| | - M Tighe
- Plant, Soil and Environment Systems, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - B R Wilson
- Plant, Soil and Environment Systems, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - I M Young
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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20
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Delgado‐Baquerizo M, Grinyer J, Reich PB, Singh BK. Relative importance of soil properties and microbial community for soil functionality: insights from a microbial swap experiment. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12674] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | - Jasmine Grinyer
- Hawkesbury Institute for the Environment Western Sydney University Penrith NSW 2751 Australia
| | - Peter B. Reich
- Hawkesbury Institute for the Environment Western Sydney University Penrith NSW 2751 Australia
- Department of Forest Resources University of Minnesota St. Paul MN 55108 USA
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment Western Sydney University Penrith NSW 2751 Australia
- Global Centre for Land‐Based Innovation Western Sydney University Penrith South DC 2751 NSW Australia
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21
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Ge Y, Priester JH, Mortimer M, Chang CH, Ji Z, Schimel JP, Holden PA. Long-Term Effects of Multiwalled Carbon Nanotubes and Graphene on Microbial Communities in Dry Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:3965-3974. [PMID: 26962674 DOI: 10.1021/acs.est.5b05620] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Little is known about the long-term effects of engineered carbonaceous nanomaterials (ECNMs) on soil microbial communities, especially when compared to possible effects of natural or industrial carbonaceous materials. To address these issues, we exposed dry grassland soil for 1 year to 1 mg g(-1) of either natural nanostructured material (biochar), industrial carbon black, three types of multiwalled carbon nanotubes (MWCNTs), or graphene. Soil microbial biomass was assessed by substrate induced respiration and by extractable DNA. Bacterial and fungal communities were examined by terminal restriction fragment length polymorphism (T-RFLP). Microbial activity was assessed by soil basal respiration. At day 0, there was no treatment effect on soil DNA or T-RFLP profiles, indicating negligible interference between the amended materials and the methods for DNA extraction, quantification, and community analysis. After a 1-year exposure, compared to the no amendment control, some treatments reduced soil DNA (e.g., biochar, all three MWCNT types, and graphene; P < 0.05) and altered bacterial communities (e.g., biochar, carbon black, narrow MWCNTs, and graphene); however, there were no significant differences across the amended treatments. These findings suggest that ECNMs may moderately affect dry soil microbial communities but that the effects are similar to those from natural and industrial carbonaceous materials, even after 1-year exposure.
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Affiliation(s)
- Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
| | | | - Monika Mortimer
- Laboratory of Environmental Toxicity, National Institute of Chemical Physics and Biophysics , Akadeemia tee 23, 12618 Tallinn, Estonia
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22
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Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments. Int J Microbiol 2016; 2016:3435809. [PMID: 26989418 PMCID: PMC4773542 DOI: 10.1155/2016/3435809] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 01/09/2016] [Accepted: 01/27/2016] [Indexed: 11/18/2022] Open
Abstract
We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole.
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23
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Rodrigues EM, Kalks KHM, Fernandes PL, Tótola MR. Bioremediation strategies of hydrocarbons and microbial diversity in the Trindade Island shoreline--Brazil. MARINE POLLUTION BULLETIN 2015; 101:517-525. [PMID: 26522160 DOI: 10.1016/j.marpolbul.2015.10.063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 10/19/2015] [Accepted: 10/23/2015] [Indexed: 06/05/2023]
Abstract
This study analyzed the microbial diversity colonizing the surface of an oil sample during its contact with water, off the Trindade Island coast and simulated the efficiency of eight different bioremediation strategies for this environment. The diversity analysis was performed using acrylic coupons that served as the support for an oil inclusion at sea. The coupons were sampled over 30 days, and T-RFLP multiplex was employed to access the diversity of fungi, Bacteria and Archaea present on the oil surface. The bioremediation strategies were simulated in a respirometer. The results showed that the bacterial domain was the most dominant in oil colonization and that the richness of the species attached to the oil gradually increases with the exposure time of the coupons. The combination of biostimulation and bioaugmentation with a native population was proven to be an effective strategy for the remediation of oil off the Trindade Island shoreline.
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Affiliation(s)
- Edmo M Rodrigues
- Laboratory of Environmental Biotechnology and Biodiversity, Microbiology Department Federal University of Viçosa, Viçosa, Minas Gerais, Brazil.
| | - Karlos H M Kalks
- Laboratory of Environmental Biotechnology and Biodiversity, Microbiology Department Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - Péricles L Fernandes
- Laboratory of Environmental Biotechnology and Biodiversity, Microbiology Department Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - Marcos R Tótola
- Laboratory of Environmental Biotechnology and Biodiversity, Microbiology Department Federal University of Viçosa, Viçosa, Minas Gerais, Brazil.
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Chang YC, Reddy MV, Umemoto H, Sato Y, Kang MH, Yajima Y, Kikuchi S. Bio-Augmentation of Cupriavidus sp. CY-1 into 2,4-D Contaminated Soil: Microbial Community Analysis by Culture Dependent and Independent Techniques. PLoS One 2015; 10:e0145057. [PMID: 26710231 PMCID: PMC4699198 DOI: 10.1371/journal.pone.0145057] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 11/29/2015] [Indexed: 11/21/2022] Open
Abstract
In the present study, a 2,4-dichlorophenoxyacetic acid (2,4-D) degrading bacterial strain CY-1 was isolated from the forest soil. Based on physiological, biochemical and 16S rRNA gene sequence analysis it was identified as Cupriavidus sp. CY-1. Further 2,4-D degradation experiments at different concentrations (200 to 800 mg l-1) were carried out using CY-1. Effect of NaCl and KNO3 on 2,4-D degradation was also evaluated. Degradation of 2,4-D and the metabolites produced during degradation process were analyzed using high pressure liquid chromatography (HPLC) and GC-MS respectively. The amount of chloride ions produced during the 2,4-D degradation were analyzed by Ion chromatography (IC) and it is stoichiometric with 2,4-D dechlorination. Furthermore two different types of soils collected from two different sources were used for 2,4-D degradation studies. The isolated strain CY-1 was bio-augmented into 2,4-D contaminated soils to analyze its degradation ability. Culture independent methods like denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP), and culture dependent methods like colony forming units (CFU) and most probable number (MPN) were used to analyze the survivability of strain CY-1 in contaminated soil. Results of T-RFLP were coincident with the DGGE analysis. From the DGGE, T-RFLP, MPN and HPLC results it was concluded that strain CY-1 effectively degraded 2,4-D without disturbing the ecosystem of soil indigenous microorganisms.
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Affiliation(s)
- Young-Cheol Chang
- Course of Chemical and Biological Engineering, Division of Sustainable and Environmental Engineering, College of Environmental Technology, Muroran Institute of Technology, 27–1 Mizumoto, Muroran, 050–8585, Japan
- * E-mail:
| | - M. Venkateswar Reddy
- Course of Chemical and Biological Engineering, Division of Sustainable and Environmental Engineering, College of Environmental Technology, Muroran Institute of Technology, 27–1 Mizumoto, Muroran, 050–8585, Japan
| | - Honoka Umemoto
- Course of Chemical and Biological Engineering, Division of Sustainable and Environmental Engineering, College of Environmental Technology, Muroran Institute of Technology, 27–1 Mizumoto, Muroran, 050–8585, Japan
| | - Yuki Sato
- Course of Chemical and Biological Engineering, Division of Sustainable and Environmental Engineering, College of Environmental Technology, Muroran Institute of Technology, 27–1 Mizumoto, Muroran, 050–8585, Japan
| | - Mi-Hye Kang
- Seoul Metropolitan Government Research Institute of Public Health and Environment, 202–3 Yangjae-dong, Seocho-gu, Seoul, 137–893, Republic of Korea
| | - Yuka Yajima
- Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto-shi, Kyoto, 606–8501, Japan
| | - Shintaro Kikuchi
- Course of Chemical and Biological Engineering, Division of Sustainable and Environmental Engineering, College of Environmental Technology, Muroran Institute of Technology, 27–1 Mizumoto, Muroran, 050–8585, Japan
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Mehmood T, Rasheed Z. Multivariate Procedure for Variable Selection and Classification of High Dimensional Heterogeneous Data. COMMUNICATIONS FOR STATISTICAL APPLICATIONS AND METHODS 2015. [DOI: 10.5351/csam.2015.22.6.575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tahir Mehmood
- Statistics, Department of Basic Sciences, Riphah International University, Pakistan
- Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Norway
| | - Zahid Rasheed
- Statistics, Department of Basic Sciences, Riphah International University, Pakistan
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Geogenic Factors as Drivers of Microbial Community Diversity in Soils Overlying Polymetallic Deposits. Appl Environ Microbiol 2015; 81:7822-32. [PMID: 26341204 DOI: 10.1128/aem.01856-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 08/29/2015] [Indexed: 12/19/2022] Open
Abstract
This study shows that the geogenic factors landform, lithology, and underlying mineral deposits (expressed by elevated metal concentrations in overlying soils) are key drivers of microbial community diversity in naturally metal-rich Australian soils with different land uses, i.e., agriculture versus natural bushland. One hundred sixty-eight soil samples were obtained from two metal-rich provinces in Australia, i.e., the Fifield Au-Pt field (New South Wales) and the Hillside Cu-Au-U rare-earth-element (REE) deposit (South Australia). Soils were analyzed using three-domain multiplex terminal-restriction-fragment-length-polymorphism (M-TRFLP) and PhyloChip microarrays. Geogenic factors were determined using field-mapping techniques and analyses of >50 geochemical parameters. At Fifield, microbial communities differed significantly with geogenic factors and equally with land use (P < 0.05). At Hillside, communities in surface soils (0.03- to 0.2-m depth) differed significantly with landform and land use (P < 0.05). Communities in deeper soils (>0.2 m) differed significantly with lithology and mineral deposit (P < 0.05). Across both sites, elevated metal contents in soils overlying mineral deposits were selective for a range of bacterial taxa, most importantly Acidobacteria, Bacilli, Betaproteobacteria, and Epsilonproteobacteria. In conclusion, long-term geogenic factors can be just as important as land use in determining soil microbial community diversity.
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Tack AJM, Laine AL, Burdon JJ, Bissett A, Thrall PH. Below-ground abiotic and biotic heterogeneity shapes above-ground infection outcomes and spatial divergence in a host-parasite interaction. THE NEW PHYTOLOGIST 2015; 207:1159-1169. [PMID: 25872137 PMCID: PMC4523403 DOI: 10.1111/nph.13408] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/13/2015] [Indexed: 05/29/2023]
Abstract
We investigated the impact of below-ground and above-ground environmental heterogeneity on the ecology and evolution of a natural plant-pathogen interaction. We combined field measurements and a reciprocal inoculation experiment to investigate the potential for natural variation in abiotic and biotic factors to mediate infection outcomes in the association between the fungal pathogen Melampsora lini and its wild flax host, Linum marginale, where pathogen strains and plant lines originated from two ecologically distinct habitat types that occur in close proximity ('bog' and 'hill'). The two habitat types differed strikingly in soil moisture and soil microbiota. Infection outcomes for different host-pathogen combinations were strongly affected by the habitat of origin of the plant lines and pathogen strains, the soil environment and their interactions. Our results suggested that tradeoffs play a key role in explaining the evolutionary divergence in interaction traits among the two habitat types. Overall, we demonstrate that soil heterogeneity, by mediating infection outcomes and evolutionary divergence, can contribute to the maintenance of variation in resistance and pathogenicity within a natural host-pathogen metapopulation.
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Affiliation(s)
- Ayco J. M. Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, PO Box 65 (Viikinkaari 1), FI-00014 University of Helsinki, Finland
| | - Anna-Liisa Laine
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, PO Box 65 (Viikinkaari 1), FI-00014 University of Helsinki, Finland
| | - Jeremy J. Burdon
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, A.C.T. 2601, Australia
| | - Andrew Bissett
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, A.C.T. 2601, Australia
| | - Peter H. Thrall
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, A.C.T. 2601, Australia
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Ding YJ, Ge CR, Yao HY. Application of substrate utilization patterns and terminal restriction fragment length polymorphism analysis to characterize the oral bacterial community of healthy subjects and patients with periodontitis. Exp Ther Med 2015; 9:2013-2017. [PMID: 26136931 DOI: 10.3892/etm.2015.2347] [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: 06/12/2014] [Accepted: 02/24/2015] [Indexed: 11/06/2022] Open
Abstract
Understanding the association between the bacterial community and oral health status is essential for the diagnosis and therapy of periodontal diseases. The aim of the present study was to apply three methods [conventional culture, substrate utilization using the MicroResp™ system and terminal restriction fragment length polymorphism (T-RFLP)] to investigate the oral bacterial community in saliva from 20 healthy subjects and 20 patients with periodontitis. The three methods all revealed that there was a systematic change in the microbial ecological characteristics associated with oral health status. Compared with the control group, the oral bacterial flora in the patients with chronic periodontitis had a greater culturable population and altered preferred carbon source and TRFLP patterns. TRFLP analysis was found to give more information and exhibit a higher sensitivity than the substrate utilization and conventional culture methods. In conclusion, TRFLP analysis is a potentially rapid method to assess the composition of the oral microbial community and for the diagnosis of chronic periodontitis.
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Affiliation(s)
- Yi-Jian Ding
- The Stomatology Medical Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Chao-Rong Ge
- Department of Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Huai-Ying Yao
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, P.R. China
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29
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Terminal Restriction Fragment Length Polymorphism Analysis of Soil Bacterial Communities under Different Vegetation Types in Subtropical Area. PLoS One 2015; 10:e0129397. [PMID: 26098851 PMCID: PMC4476674 DOI: 10.1371/journal.pone.0129397] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/07/2015] [Indexed: 11/19/2022] Open
Abstract
Soil microbes are active players in energy flow and material exchange of the forest ecosystems, but the research on the relationship between the microbial diversity and the vegetation types is less conducted, especially in the subtropical area of China. In this present study, the rhizosphere soils of evergreen broad-leaf forest (EBF), coniferous forest (CF), subalpine dwarf forest (SDF) and alpine meadow (AM) were chosen as test sites. Terminal-restriction fragment length polymorphisms (T-RFLP) analysis was used to detect the composition and diversity of soil bacterial communities under different vegetation types in the National Natural Reserve of Wuyi Mountains. Our results revealed distinct differences in soil microbial composition under different vegetation types. Total 73 microbes were identified in soil samples of the four vegetation types, and 56, 49, 46 and 36 clones were obtained from the soils of EBF, CF, SDF and AM, respectively, and subsequently sequenced. The Actinobacteria, Fusobacterium, Bacteroidetes and Proteobacteria were the most predominant in all soil samples. The order of Shannon-Wiener index (H) of all soil samples was in the order of EBF>CF>SDF>AM, whereas bacterial species richness as estimated by four restriction enzymes indicated no significant difference. Principal component analysis (PCA) revealed that the soil bacterial communities’ structures of EBF, CF, SDF and AM were clearly separated along the first and second principal components, which explained 62.17% and 31.58% of the total variance, respectively. The soil physical-chemical properties such as total organic carbon (TOC), total nitrogen (TN), total phosphorus (TP) and total potassium (TK) were positively correlated with the diversity of bacterial communities.
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30
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Welz PJ, Palmer Z, Isaacs S, Kirby B, le Roes-Hill M. Analysis of substrate degradation, metabolite formation and microbial community responses in sand bioreactors treating winery wastewater: a comparative study. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2014; 145:147-156. [PMID: 25026370 DOI: 10.1016/j.jenvman.2014.06.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/25/2014] [Accepted: 06/26/2014] [Indexed: 06/03/2023]
Abstract
There is a global need for the implementation of more cost-effective green technologies for the treatment of effluent from wineries. However, systems reliant on microbial biodegradation may be adversely affected by the highly seasonal character of cellar waste. In this study, the biodegradation of two different formulations of winery effluent in sand bioreactors was compared. The degradation of organic substrates and formation of metabolites was monitored by physicochemical analyses of pore water and final effluent samples. Changes in the bacterial community structures were detected using molecular fingerprinting. In wastewater with an overall COD of 2027 mg/L, a formulation with a high concentration of acetate (800 mg COD/L) was more recalcitrant to degradation than a formulation with a high concentration of glucose (800 mg COD/L). Ethanol, glucose and phenolics were degraded preferentially in the deeper layers of the sand bioreactors (average Eh 25 mV) than in the superficial layers (average Eh 102 mV). The redox status also played a pivotal role on the bacterial community composition. The study yielded valuable insight that can be utilized in the design (configuration and operation) of full scale sand bioreactors.
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Affiliation(s)
- P J Welz
- Biocatalysis and Technical Biology (BTB) Research Group, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa.
| | - Z Palmer
- Biocatalysis and Technical Biology (BTB) Research Group, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa; Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville 7535, South Africa.
| | - S Isaacs
- Biocatalysis and Technical Biology (BTB) Research Group, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa.
| | - B Kirby
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville 7535, South Africa.
| | - M le Roes-Hill
- Biocatalysis and Technical Biology (BTB) Research Group, Cape Peninsula University of Technology, PO Box 1906, Bellville 7535, South Africa.
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Chen Q, Qi L, Bi Q, Dai P, Sun D, Sun C, Liu W, Lu L, Ni W, Lin X. Comparative effects of 3,4-dimethylpyrazole phosphate (DMPP) and dicyandiamide (DCD) on ammonia-oxidizing bacteria and archaea in a vegetable soil. Appl Microbiol Biotechnol 2014; 99:477-87. [PMID: 25172135 DOI: 10.1007/s00253-014-6026-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 08/05/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022]
Abstract
Nitrification inhibitors (NIs) 3,4-dimethylpyrazole phosphate (DMPP) and dicyandiamide (DCD) have been used extensively to improve nitrogen fertilizer utilization in farmland. However, their comparative effects on ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in agricultural soils are still unclear. Here, we compared the impacts of these two inhibitors on soil nitrification, AOA and AOB abundance as well as their community structure in a vegetable soil by using real-time PCR and terminal restriction fragment length polymorphism (T-RFLP). Our results showed that urea application significantly increased the net nitrification rates, but were significantly inhibited by both NIs, and the inhibitory effect of DMPP was significantly greater than that of DCD. AOB growth was more greatly inhibited by DMPP than by DCD, and the net nitrification rate was significantly related to AOB abundance, but not to AOA abundance. Application of urea and NIs to soil did not change the diversity of the AOA community, with the T-RFs remaining in proportions that were similar to control soils, while the community structure of AOB exhibited obvious shifts within all different treatments compared to the control. Phylogenetic analysis showed that all AOA sequences fell within group 1.1a and group 1.1b, and the AOB community consisted of Nitrosospira cluster 3, cluster 0, and unidentified species. These results suggest that DMPP exhibited a stronger inhibitory effect on nitrification than DCD by inhibiting AOB rather than AOA.
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Affiliation(s)
- Qiuhui Chen
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
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32
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Macdonald CA, Crawley MJ, Wright DJ, Kuczynski J, Robinson L, Knight R, Al-Soud WA, Sørensen SJ, Deng Y, Zhou J, Singh BK. Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment. Environ Microbiol 2014; 17:841-54. [PMID: 24935069 DOI: 10.1111/1462-2920.12539] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/09/2014] [Indexed: 11/30/2022]
Abstract
Herbivory is an important modulator of plant biodiversity and productivity in grasslands, but our understanding of herbivore-induced changes on below-ground processes and communities is limited. Using a long-term (17 years) experimental site, we evaluated impacts of rabbit and invertebrate grazers on some soil functions involved in carbon cycling, microbial diversity, structure and functional composition. Both rabbit and invertebrate grazing impacted soil functions and microbial community structure. All functional community measures (functions, biogeochemical cycling genes, network association between different taxa) were more strongly affected by invertebrate grazers than rabbits. Furthermore, our results suggest that exclusion of invertebrate grazers decreases both microbial biomass and abundance of genes associated with key biogeochemical cycles, and could thus have long-term consequences for ecosystem functions. The mechanism behind these impacts are likely to be driven by both direct effects of grazing altering the pattern of nutrient inputs and by indirect effects through changes in plant species composition. However, we could not entirely discount that the pesticide used to exclude invertebrates may have affected some microbial community measures. Nevertheless, our work illustrates that human activity that affects grazing intensity may affect ecosystem functioning and sustainability, as regulated by multi-trophic interactions between above- and below-ground communities.
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Affiliation(s)
- Catriona A Macdonald
- Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, NSW, Australia
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Nagarajan K, Loh KC. Molecular biology-based methods for quantification of bacteria in mixed culture: perspectives and limitations. Appl Microbiol Biotechnol 2014; 98:6907-19. [DOI: 10.1007/s00253-014-5870-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/30/2014] [Accepted: 05/31/2014] [Indexed: 02/07/2023]
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Cregger MA, Sanders NJ, Dunn RR, Classen AT. Microbial communities respond to experimental warming, but site matters. PeerJ 2014; 2:e358. [PMID: 24795850 PMCID: PMC4006228 DOI: 10.7717/peerj.358] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/02/2014] [Indexed: 11/20/2022] Open
Abstract
Because microorganisms are sensitive to temperature, ongoing global warming is predicted to influence microbial community structure and function. We used large-scale warming experiments established at two sites near the northern and southern boundaries of US eastern deciduous forests to explore how microbial communities and their function respond to warming at sites with differing climatic regimes. Soil microbial community structure and function responded to warming at the southern but not the northern site. However, changes in microbial community structure and function at the southern site did not result in changes in cellulose decomposition rates. While most global change models rest on the assumption that taxa will respond similarly to warming across sites and their ranges, these results suggest that the responses of microorganisms to warming may be mediated by differences across the geographic boundaries of ecosystems.
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Affiliation(s)
- Melissa A Cregger
- Department of Ecology and Evolutionary Biology, University of Tennessee , Knoxville, TN , USA
| | - Nathan J Sanders
- Department of Ecology and Evolutionary Biology, University of Tennessee , Knoxville, TN , USA ; The Natural History Museum of Denmark, University of Copenhagen , Copenhagen , Denmark
| | - Robert R Dunn
- Department of Biological Sciences, North Carolina State University , Raleigh, NC , USA
| | - Aimée T Classen
- Department of Ecology and Evolutionary Biology, University of Tennessee , Knoxville, TN , USA ; The Natural History Museum of Denmark, University of Copenhagen , Copenhagen , Denmark
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van Dorst J, Bissett A, Palmer AS, Brown M, Snape I, Stark JS, Raymond B, McKinlay J, Ji M, Winsley T, Ferrari BC. Community fingerprinting in a sequencing world. FEMS Microbiol Ecol 2014; 89:316-30. [DOI: 10.1111/1574-6941.12308] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 02/13/2014] [Accepted: 02/18/2014] [Indexed: 01/25/2023] Open
Affiliation(s)
- Josie van Dorst
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW Australia
| | | | - Anne S. Palmer
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Mark Brown
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW Australia
| | - Ian Snape
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Jonathan S. Stark
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Ben Raymond
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - John McKinlay
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Mukan Ji
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW Australia
| | - Tristrom Winsley
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW Australia
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Singh BK, Quince C, Macdonald CA, Khachane A, Thomas N, Al-Soud WA, Sørensen SJ, He Z, White D, Sinclair A, Crooks B, Zhou J, Campbell CD. Loss of microbial diversity in soils is coincident with reductions in some specialized functions. Environ Microbiol 2014; 16:2408-20. [DOI: 10.1111/1462-2920.12353] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 11/30/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Brajesh K. Singh
- Hawkesbury Institute for the Environment; University of Western Sydney; Penrith NSW Australia
| | | | - Catriona A. Macdonald
- Hawkesbury Institute for the Environment; University of Western Sydney; Penrith NSW Australia
| | - Amit Khachane
- Hawkesbury Institute for the Environment; University of Western Sydney; Penrith NSW Australia
| | | | - Waleed Abu Al-Soud
- Department of Biology; Faculty of Science; University of Copenhagen; Copenhagen Denmark
| | - Søren J. Sørensen
- Department of Biology; Faculty of Science; University of Copenhagen; Copenhagen Denmark
| | - Zhili He
- Department of Botany and Microbiology; Institute for Environmental Genomics; Stephenson Research and Technology Centre; University of Oklahoma; Norman OK USA
| | | | | | - Bill Crooks
- SRUC Auchincruive; Ayr Auchincruive Estate UK
| | - Jizhong Zhou
- Department of Botany and Microbiology; Institute for Environmental Genomics; Stephenson Research and Technology Centre; University of Oklahoma; Norman OK USA
| | - Colin D. Campbell
- The James Hutton Institute; Aberdeen UK
- Department of Soil and Environment; Swedish Agricultural Sciences University; Uppsala Sweden
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37
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Osborne CA. Terminal restriction fragment length polymorphism (T-RFLP) profiling of bacterial 16S rRNA genes. Methods Mol Biol 2014; 1096:57-69. [PMID: 24515360 DOI: 10.1007/978-1-62703-712-9_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
T-RFLP profiling is a very effective method for comparing many samples in an environmental microbiology study, because fingerprints of microbial diversity can be generated in a sensitive, reproducible, and cost-effective manner. This protocol describes the steps required to generate T-RFLP profiles of the dominant members of a bacterial community, by PCR amplification of the bacterial 16S rRNA genes and three restriction endonuclease digests to generate three different profiles for each sample. The generation of multiple profiles per sample provides enough information to confidently differentiate rich environmental bacterial communities.
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Affiliation(s)
- Catherine A Osborne
- Department of Civil Engineering, Centre for Water Sensitive Cities, Monash University, Clayton, VIC, Australia
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38
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Pervin HM, Dennis PG, Lim HJ, Tyson GW, Batstone DJ, Bond PL. Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors. WATER RESEARCH 2013; 47:7098-7108. [PMID: 24216229 DOI: 10.1016/j.watres.2013.07.053] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 07/02/2013] [Accepted: 07/04/2013] [Indexed: 06/02/2023]
Abstract
Temperature-phased anaerobic digestion (TPAD) is an emerging technology that facilitates improved performance and pathogen destruction in anaerobic sewage sludge digestion by optimising conditions for 1) hydrolytic and acidogenic organisms in a first-stage/pre-treatment reactor and then 2) methogenic populations in a second stage reactor. Pre-treatment reactors are typically operated at 55-65 °C and as such select for thermophilic bacterial communities. However, details of key microbial populations in hydrolytic communities and links to functionality are very limited. In this study, experimental thermophilic pre-treatment (TP) and control mesophilic pre-treatment (MP) reactors were operated as first-stages of TPAD systems treating activated sludge for 340 days. The TP system was operated sequentially at 50, 60 and 65 °C, while the MP rector was held at 35 °C for the entire period. The composition of microbial communities associated with the MP and TP pre-treatment reactors was characterised weekly using terminal-restriction fragment length polymorphism (T-RFLP) supported by clone library sequencing of 16S rRNA gene amplicons. The outcomes of this approach were confirmed using 454 pyrosequencing of gene amplicons and fluorescence in-situ hybridisation (FISH). TP associated bacterial communities were dominated by populations affiliated to the Firmicutes, Thermotogae, Proteobacteria and Chloroflexi. In particular there was a progression from Thermotogae to Lutispora and Coprothermobacter and diversity decreased as temperature and hydrolysis performance increased. While change in the composition of TP associated bacterial communities was attributable to temperature, that of MP associated bacterial communities was related to the composition of the incoming feed. This study determined processes driving the dynamics of key microbial populations that are correlated with an enhanced hydrolytic functionality of the TPAD system.
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Affiliation(s)
- Hasina M Pervin
- Advanced Water Management Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
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Characteristics of foliar fungal endophyte assemblages and host effective components in Salvia miltiorrhiza Bunge. Appl Microbiol Biotechnol 2013; 98:3143-55. [DOI: 10.1007/s00253-013-5300-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/24/2013] [Accepted: 09/27/2013] [Indexed: 01/02/2023]
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40
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O’Neill T, Balks M, Stevenson B, López-Martínez J, Aislabie J, Rhodes P. The short-term effects of surface soil disturbance on soil bacterial community structure at an experimental site near Scott Base, Antarctica. Polar Biol 2013. [DOI: 10.1007/s00300-013-1322-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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41
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Rodrigues DF, Jaisi DP, Elimelech M. Toxicity of functionalized single-walled carbon nanotubes on soil microbial communities: implications for nutrient cycling in soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:625-633. [PMID: 23205469 DOI: 10.1021/es304002q] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Culture-dependent and -independent methods were employed to determine the impact of carboxyl-functionalized single-walled carbon nanotubes (SWNTs) on fungal and bacterial soil microbial communities. Soil samples were exposed to 0 (control), 250, and 500 μg of SWNTs per gram of soil. Aliquots of soil were sampled for up to 14 days for culture-dependent analyses, namely, plate count agar and bacterial community level physiological profiles, and culture-independent analyses, namely, quantitative real-time polymerase chain reaction (qPCR), mutliplex-terminal restriction fragment length polymorphism (M-TRFLP), and clone libraries. Results from culture-independent and -dependent methods show that the bacterial soil community is transiently affected by the presence of SWNTs. The major impact of SWNTs on bacterial community was observed after 3 days of exposure, but the bacterial community completely recovered after 14 days. However, no recovery of the fungal community was observed for the duration of the experiment. Physiological and DNA microbial community analyses suggest that fungi and bacteria involved in carbon and phosphorus biogeochemical cycles can be adversely affected by the presence of SWNTs. This study suggests that high concentrations of SWNTs can have widely varying effects on microbial communities and biogeochemical cycling of nutrients in soils.
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Affiliation(s)
- Debora F Rodrigues
- Department of Civil and Environmental Engineering, University of Houston, Houston, Texas 77204-5003, United States.
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Cregger MA, Schadt CW, McDowell NG, Pockman WT, Classen AT. Response of the soil microbial community to changes in precipitation in a semiarid ecosystem. Appl Environ Microbiol 2012; 78:8587-94. [PMID: 23023755 PMCID: PMC3502934 DOI: 10.1128/aem.02050-12] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 09/24/2012] [Indexed: 11/20/2022] Open
Abstract
Microbial communities regulate many belowground carbon cycling processes; thus, the impact of climate change on the structure and function of soil microbial communities could, in turn, impact the release or storage of carbon in soils. Here we used a large-scale precipitation manipulation (+18%, -50%, or ambient) in a piñon-juniper woodland (Pinus edulis-Juniperus monosperma) to investigate how changes in precipitation amounts altered soil microbial communities as well as what role seasonal variation in rainfall and plant composition played in the microbial community response. Seasonal variability in precipitation had a larger role in determining the composition of soil microbial communities in 2008 than the direct effect of the experimental precipitation treatments. Bacterial and fungal communities in the dry, relatively moisture-limited premonsoon season were compositionally distinct from communities in the monsoon season, when soil moisture levels and periodicity varied more widely across treatments. Fungal abundance in the drought plots during the dry premonsoon season was particularly low and was 4.7 times greater upon soil wet-up in the monsoon season, suggesting that soil fungi were water limited in the driest plots, which may result in a decrease in fungal degradation of carbon substrates. Additionally, we found that both bacterial and fungal communities beneath piñon pine and juniper were distinct, suggesting that microbial functions beneath these trees are different. We conclude that predicting the response of microbial communities to climate change is highly dependent on seasonal dynamics, background climatic variability, and the composition of the associated aboveground community.
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Affiliation(s)
- Melissa A Cregger
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA.
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Elliott GN, Thomas N, Macrae M, Campbell CD, Ogden ID, Singh BK. Multiplex T-RFLP allows for increased target number and specificity: detection of Salmonella enterica and six species of Listeria in a single test. PLoS One 2012; 7:e43672. [PMID: 22937073 PMCID: PMC3427147 DOI: 10.1371/journal.pone.0043672] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/24/2012] [Indexed: 01/14/2023] Open
Abstract
A multiplex T-RFLP test was developed to detect and identify Salmonella enterica and all six species of Listeria inoculated into milk at minimal levels. Extensive in silico analysis was used to design a fifteen-primer, six-amplimer methodology and in vitro application showed target organism DNA, when amplified individually, yielded the predicted terminal restriction fragments (TRFs) following digestion. Non-target organisms were either not-amplified or yielded TRFs which did not interfere with target identification. Multiple target DNA analysis gave over 86% detection of total TRFs predicted, and this was improved to over 90% detection of total TRFs predicted when only two target DNA extracts were combined analysed. Co-inoculation of milk with five strains each of the target species of S. enterica and L. monocytogenes, along with five strains of the non-target species E. coli was followed by enrichment in SEL medium for M-TRFLP analysis. This allowed for detection of both target species in all samples, with detection of one S. enterica and two Listeria TRFs in all cases, and detection of a second S. enterica TRF in 91% of cases. This was from an initial inoculum of <5 cfu per 25 ml milk with a background of competing E. coli present, and gave a result from sampling of under 20 hours. The ability to increase target species number without loss of sensitivity means that extensive screening can be performed at reduced cost due to a reduction in the number of tests required.
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Birnbaum C, Barrett LG, Thrall PH, Leishman MR. Mutualisms are not constraining cross-continental invasion success of Acacia species within Australia. DIVERS DISTRIB 2012. [DOI: 10.1111/j.1472-4642.2012.00920.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Christina Birnbaum
- Department of Biological Sciences; Macquarie University; North Ryde; NSW; 2109; Australia
| | - Luke G. Barrett
- CSIRO Plant Industry; GPO Box 1600; Canberra; ACT; 2601; Australia
| | - Peter H. Thrall
- CSIRO Plant Industry; GPO Box 1600; Canberra; ACT; 2601; Australia
| | - Michelle R. Leishman
- Department of Biological Sciences; Macquarie University; North Ryde; NSW; 2109; Australia
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Reith F, Brugger J, Zammit CM, Gregg AL, Goldfarb KC, Andersen GL, DeSantis TZ, Piceno YM, Brodie EL, Lu Z, He Z, Zhou J, Wakelin SA. Influence of geogenic factors on microbial communities in metallogenic Australian soils. ISME JOURNAL 2012; 6:2107-18. [PMID: 22673626 DOI: 10.1038/ismej.2012.48] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Links between microbial community assemblages and geogenic factors were assessed in 187 soil samples collected from four metal-rich provinces across Australia. Field-fresh soils and soils incubated with soluble Au(III) complexes were analysed using three-domain multiplex-terminal restriction fragment length polymorphism, and phylogenetic (PhyloChip) and functional (GeoChip) microarrays. Geogenic factors of soils were determined using lithological-, geomorphological- and soil-mapping combined with analyses of 51 geochemical parameters. Microbial communities differed significantly between landforms, soil horizons, lithologies and also with the occurrence of underlying Au deposits. The strongest responses to these factors, and to amendment with soluble Au(III) complexes, was observed in bacterial communities. PhyloChip analyses revealed a greater abundance and diversity of Alphaproteobacteria (especially Sphingomonas spp.), and Firmicutes (Bacillus spp.) in Au-containing and Au(III)-amended soils. Analyses of potential function (GeoChip) revealed higher abundances of metal-resistance genes in metal-rich soils. For example, genes that hybridised with metal-resistance genes copA, chrA and czcA of a prevalent aurophillic bacterium, Cupriavidus metallidurans CH34, occurred only in auriferous soils. These data help establish key links between geogenic factors and the phylogeny and function within soil microbial communities. In particular, the landform, which is a crucial factor in determining soil geochemistry, strongly affected microbial community structures.
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Affiliation(s)
- Frank Reith
- School of Earth and Environmental Sciences, Centre of Tectonics, Resources and Exploration (TRaX), The University of Adelaide, North Terrace, South Australia, Australia.
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46
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Stutter MI, Richards S. Relationships between soil physicochemical, microbiological properties, and nutrient release in buffer soils compared to field soils. JOURNAL OF ENVIRONMENTAL QUALITY 2012; 41:400-409. [PMID: 22370402 DOI: 10.2134/jeq2010.0456] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The retention of nutrients in narrow, vegetated riparian buffer strips (VBS) is uncertain and underlying processes are poorly understood. Evidence suggests that buffer soils are poor at retaining dissolved nutrients, especially phosphorus (P), necessitating management actions if P retention is not to be compromised. We sampled 19 buffer strips and adjacent arable field soils. Differences in nutrient retention between buffer and field soils were determined using a combined assay for release of dissolved P, N, and C forms and particulate P. We then explored these differences in relation to changes in soil bulk density (BD), moisture, organic matter by loss on ignition (OM), and altered microbial diversity using molecular fingerprinting (terminal restriction fragment length polymorphism [TRFLP]). Buffer soils had significantly greater soil OM (89% of sites), moisture content (95%), and water-soluble nutrient concentrations for dissolved organic C (80%), dissolved organic N (80%), dissolved organic P (55%), and soluble reactive P (70%). Buffer soils had consistently smaller bulk densities than field soils. Soil fine particle release was generally greater for field than buffer soils. Significantly smaller soil bulk density in buffer soils than in adjacent fields indicated increased porosity and infiltration in buffers. Bacterial, archaeal, and fungal communities showed altered diversity between the buffer and field soils, with significant relationships with soil BD, moisture, OM, and increased solubility of buffer nutrients. Current soil conditions in VBS appear to be leading to potentially enhanced nutrient leaching via increasing solubility of C, N, and P. Manipulating soil microbial conditions (by management of soil moisture, vegetation type, and cover) may provide options for increasing the buffer storage for key nutrients such as P without increasing leaching to adjacent streams.
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Crawford JW, Deacon L, Grinev D, Harris JA, Ritz K, Singh BK, Young I. Microbial diversity affects self-organization of the soil-microbe system with consequences for function. J R Soc Interface 2011; 9:1302-10. [PMID: 22158839 DOI: 10.1098/rsif.2011.0679] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Soils are complex ecosystems and the pore-scale physical structure regulates key processes that support terrestrial life. These include maintaining an appropriate mixture of air and water in soil, nutrient cycling and carbon sequestration. There is evidence that this structure is not random, although the organizing mechanism is not known. Using X-ray microtomography and controlled microcosms, we provide evidence that organization of pore-scale structure arises spontaneously out of the interaction between microbial activity, particle aggregation and resource flows in soil. A simple computational model shows that these interactions give rise to self-organization involving both physical particles and microbes that gives soil unique material properties. The consequence of self-organization for the functioning of soil is determined using lattice Boltzmann simulation of fluid flow through the observed structures, and predicts that the resultant micro-structural changes can significantly increase hydraulic conductivity. Manipulation of the diversity of the microbial community reveals a link between the measured change in micro-porosity and the ratio of fungal to bacterial biomass. We suggest that this behaviour may play an important role in the way that soil responds to management and climatic change, but that this capacity for self-organization has limits.
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Affiliation(s)
- John W Crawford
- Faculty of Agriculture, Food and Natural Resources, University of Sydney, Sydney, New South Wales 2006, Australia.
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Nishizawa T, Zhaorigetu, Komatsuzaki M, Sato Y, Kaneko N, Ohta H. Molecular characterization of fungal communities in non-tilled, cover-cropped upland rice field soils. Microbes Environ 2011; 25:204-10. [PMID: 21597240 DOI: 10.1264/jsme2.me10108] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This study aimed to characterize soil fungal communities in upland rice fields managed with tillage/non-tillage and winter cover-cropping (hairy vetch and cereal rye) practices, using PCR-based molecular methods. The study plots were maintained as upland fields for 5 years and the soils sampled in the second and fifth years were analyzed using T-RFLP (terminal restriction fragment length polymorphism) profiling and clone libraries with the internal transcribed spacer (ITS) region and domain 1 (D1) of the fungal large-subunit (fLSU) rRNA (D1(fLSU)) as the target DNA sequence. From the 2nd-year-sample, 372 cloned sequences of fungal ITS-D1(fLSU) were obtained and clustered into 80 nonredundant fungal OTUs (operational taxonomic units) in 4 fungal phyla. The T-RFLP profiling was performed with the 2nd- and 5th-year-samples and the major T-RFs (terminal restriction fragments) were identified using a theoretical fragment analysis of the ITS-D1(fLSU) clones. These molecular analyses showed that the fungal community was influenced more strongly by the cover-cropping than tillage practices. Moreover, the non-tilled, cover-cropped soil was characterized by a predominance of Cryptococcus sp. in the phylum Basidiomycota. We provided a genetic database of the fungal ITS-D1(fLSU)s in the differently managed soils of upland rice fields.
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Affiliation(s)
- Tomoyasu Nishizawa
- Ibaraki University College of Agriculture, 3–21–1 Chuou, Ami-machi, Ibaraki 300–0393, Japan.
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Links between ammonia oxidizer community structure, abundance, and nitrification potential in acidic soils. Appl Environ Microbiol 2011; 77:4618-25. [PMID: 21571885 DOI: 10.1128/aem.00136-11] [Citation(s) in RCA: 297] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ammonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen fertilization strategies. AOA and AOB abundance and community composition were therefore investigated in tea soils and adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of respective ammonia monooxygenase (amoA) genes. There was strong evidence that soil pH was an important factor controlling AOB but not AOA abundance, and the ratio of AOA to AOB amoA gene abundance increased with decreasing soil pH in the tea orchard soils. In contrast, T-RFLP analysis suggested that soil pH was a key explanatory variable for both AOA and AOB community structure, but a significant relationship between community abundance and nitrification potential was observed only for AOA. High potential nitrification rates indicated that nitrification was mainly driven by AOA in these acidic soils. Dominant AOA amoA sequences in the highly acidic tea soils were all placed within a specific clade, and one AOA genotype appears to be well adapted to growth in highly acidic soils. Specific AOA and AOB populations dominated in soils at particular pH values and N content, suggesting adaptation to specific niches.
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50
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Hua L, Chen Y, Wu W, Ma H. Microorganism communities and chemical characteristics in sludge-bamboo charcoal composting system. ENVIRONMENTAL TECHNOLOGY 2011; 32:663-672. [PMID: 21877547 DOI: 10.1080/09593330.2010.510534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Microorganism communities and chemical characteristics in sludge-bamboo charcoal composting system were investigated to find the effect of bamboo charcoal on composting. According to a plate count test, abundances of bacteria, fungi and actinomycetes in the treatment with bamboo charcoal were several times higher than those in treatment without bamboo charcoal. In addition, terminal restriction fragment length polymorphism (TRFLP) analysis indicated that the bacterial community diversity in treatment with bamboo charcoal was greater than that of the control. Both results demonstrated that amendment with bamboo charcoal can increase microorganism population and microorganism community diversity in a sludge composting system. Moreover, the results of FTIR spectroscopy disclosed that aerobic composting can promote the formation of surface acid groups on bamboo charcoal. These surface acid groups may deprotonate and react with NH4+ to form stable complexes. Therefore, the increase of functional groups accompanied with greater assimilation of nitrogen by microorganisms could reduce nitrogen loss in sludge composting.
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MESH Headings
- Bambusa/chemistry
- Charcoal/chemistry
- Cluster Analysis
- Colony Count, Microbial
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- Sewage/chemistry
- Sewage/microbiology
- Soil/chemistry
- Spectroscopy, Fourier Transform Infrared
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Affiliation(s)
- Li Hua
- College of Resource and Environment, Shaanxi University of Science and Technology, Xi'an 710021, China.
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