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Tatsumi C, Azuma WA, Ogawa Y, Komada N. Nitrogen Availability and Microbial Communities of Canopy Soils in a Large Cercidiphyllum japonicum Tree of a Cool-Temperate Old Growth Forest. MICROBIAL ECOLOGY 2021; 82:919-931. [PMID: 33606088 DOI: 10.1007/s00248-021-01707-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
Canopy soils on large trees are important for supporting the lives of many canopy plants, and thereby increasing regional biodiversity. However, because of the less accessibility to canopy soils, there is insufficient knowledge on how canopy soils produce available nitrogen (N) for canopy plants through the activity of canopy soil microbes. Canopy soils usually have different soil properties from ground soils, so we hypothesized that canopy soils would have unique microbial communities compared to ground soils, but still provide available N for canopy plants. Here, we compared soil N availability, including net N mineralization and nitrification rate, and microbial communities between canopy soils (organic soils) collected at various heights of a large Cercidiphyllum japonicum tree and ground soils (organic and mineral soils) in a cool-temperate old-growth forest of Japan. The canopy soils had significantly different N availability (mass-based higher but volume-based lower) and microbial communities from the ground mineral soils. Among organic soils, the height of the soil had an impact on the microbial communities but not on the N availability, which agreed with our hypothesis. Despite the decrease in fungal abundance in the higher soils, the increase in certain components of the cellulose-decomposing fungi and oligotrophic bacteria may contribute to the available N production. Also, the abundance of ammonia-oxidizers did not change with the height, which would be important for the nitrification rate. Our study implied canopy soils could provide N to canopy plants partly through the functional redundancy within different microbial communities and constant population of ammonia-oxidizers.
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Affiliation(s)
- Chikae Tatsumi
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | - Wakana A Azuma
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
- Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, 657-8501, Japan.
| | - Yuya Ogawa
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Natsuki Komada
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
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2
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Eskov AK, Zverev AO, Abakumov EV. Microbiomes in Suspended Soils of Vascular Epiphytes Differ from Terrestrial Soil Microbiomes and from Each Other. Microorganisms 2021; 9:microorganisms9051033. [PMID: 34064848 PMCID: PMC8150705 DOI: 10.3390/microorganisms9051033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 01/04/2023] Open
Abstract
Microbial biodiversity parameters for tropical rainforests remain poorly understood. Whilst the soil microbiome accounts up to 95% of the total diversity of microorganisms in terrestrial ecosystems, the microbiome of suspended soils formed by vascular epiphytes remains completely unexplored. Samples of ground and suspended soils were collected in Cat Tien National Park, southern Vietnam. DNA extraction and sequencing were performed, and libraries of 16s rDNA gene sequences were analyzed. Alpha diversity indices of the microorganisms were the highest in the forest ground soil. In general, the microbiological diversity of all the soil types was found to be similar at the phylum level. Taxonomic composition of the bacterial communities in the suspended soils of plants from the same species are not closer than the taxonomic compositions of the communities in the suspended soils of different plant species. However, the beta diversity analysis revealed significant differences in the movement of mineral elements in terrestrial versus suspended soils. Our data showed that the suspended soils associated with vascular epiphytes were a depository of unique microbiological biodiversity. A contributing factor was the presence of large amounts of organic matter in the suspended soils-deposits collected by the epiphytes-which would have been degraded by termites if it had reached the ground. Further, the nutrient content of the suspended soils was prime for soil respiration activity and taxonomic microbial community biodiversity.
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Affiliation(s)
- Alen K. Eskov
- Faculty of Biology, Lomonosov Moscow State University, 1–12 Leninskie Gory, 119991 Moscow, Russia
- Tzitzin Main Botanical Garden, Russian Academy of Sciences, 4 Botanicheskaya ul., 117628 Moscow, Russia
- Correspondence:
| | - Alexei O. Zverev
- Faculty of Biology, Saint-Petersburg State University, 7/9 Universitetskaya nab., 199034 St. Petersburg, Russia; (A.O.Z.); (E.V.A.)
- All-Russian Research Institute for Agricultural Microbiology, 3 Podbelsky chausse, 196608 St. Petersburg, Russia
| | - Evgeny V. Abakumov
- Faculty of Biology, Saint-Petersburg State University, 7/9 Universitetskaya nab., 199034 St. Petersburg, Russia; (A.O.Z.); (E.V.A.)
- All-Russian Research Institute for Agricultural Microbiology, 3 Podbelsky chausse, 196608 St. Petersburg, Russia
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3
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Liu Z, Zhou H, Xie W, Yang Z, Lv Q. Long-term effects of maize straw return and manure on the microbial community in cinnamon soil in Northern China using 16S rRNA sequencing. PLoS One 2021; 16:e0249884. [PMID: 33886593 PMCID: PMC8062091 DOI: 10.1371/journal.pone.0249884] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 03/26/2021] [Indexed: 11/30/2022] Open
Abstract
Excessive use of chemical fertilizers in agricultural practices have demonstrated a significant impact on microbial diversity and community in soil by altering soil physical and chemical properties, thereby leading to a certain degree of soil salinization and nutritional imbalances. As an organic amendment, maize straw has been widely used to improve soil quality; however, its effect on the soil bacterial community remains limited in Calcarie-Fluvie Cambisols soil in semi-humid arid plateau of North China. In the present experiment, we investigated the effects of continuous straw utilization and fertilization on bacterial communities in Shouyang, Shanxi province, China. Soil samples were collected from 5 different straw utilization and fertilization modes in the following ways: straw mulching (SM), straw crushing (SC), cattle manure (CM), in which way straw is firstly used as silage and then organic fertilizer, control with no straw return (NSR), and control without fertilizers (CK), same amount of N+P fertilizer was applied to the regimes except CK. High-throughput sequencing approaches were applied to the V3-V4 regions of the 16S ribosomal RNA for analysis of the bacterial abundance and community structures. Different long-term straw returning regimes significantly altered the physicochemical properties and bacterial communities of soil, among which CM had the most significant effects on soil fertility and bacterial diversity. Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes were consistently dominant in all soil samples, and Redundancy analysis (RDA) showed significant association of total nitrogen (TN), total phosphorus (TP) and available potassium (AK) with alternation of the bacterial community. Cattle manure had the most beneficial effects on soil fertility and bacterial diversity among different straw utilization and fertilization modes.
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Affiliation(s)
- Zhiping Liu
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan, P. R. China
| | - Huaiping Zhou
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan, P. R. China
- * E-mail:
| | - Wenyan Xie
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan, P. R. China
| | - Zhenxing Yang
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan, P. R. China
| | - Qianqian Lv
- College of Biological Engineering, Shanxi University, Taiyuan, P. R. China
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4
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Nie H, Qin T, Yan D, Lv X, Wang J, Huang Y, Lv Z, Liu S, Liu F. How do tree species characteristics affect the bacterial community structure of subtropical natural mixed forests? THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:144633. [PMID: 33387765 DOI: 10.1016/j.scitotenv.2020.144633] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/14/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
The effects of tree species on bacterial community structure have attracted much attention, but few studies have been done in natural mixed forests. In this study, we selected 12 sampling sites in the subtropical natural mixed forest (mainly distributed by Chinese sweet gum, chestnut, Oriental oak, Masson pine, Chinese fir, etc.). The fermentation layer (OF) and humified layer (OH) were mixed as forest floor samples, and the topsoil samples (0-10 cm) were taken. Bacterial composition was studied by 16S rRNA gene sequencing. Coniferous canopy area ratio (Pc), broadleaved and shrubby canopy area ratio (Phwd), elevation, soil properties were tested. The objective is to reveal which soil properties are significantly affected by tree species characteristics, which soil properties significantly affect bacterial community structure, and whether the bacterial community structure is the same in forest floor and topsoil samples at the same sampling site. The results showed that: (1) Pc and Phwd could be used to represent tree species characteristics of natural mixed forests, and they significantly (P=0.05) affected the soil C/N ratio; (2) the soil C/N ratio was the main factor affecting the soil bacterial community composition, especially for the dominant heterotrophic bacteria (Acidothermus, Variibacter, Candidatus Solibacter, Acidibacter, and Bryobacter). The relative abundance (1.11-26.27%) of the dominant heterotrophic bacteria increases with an increase in the C/N ratio (6.33-10.76) within a certain range; (3) the dominant bacteria in topsoil samples were Nitrospira, Acidothermus, Arthrobacter, Bradyrhizobium, and Variibacter, while that in forest floor samples were Jatrophihabitans, Acidothermus, Burkholderia-Paraburkholderia, and Bradyrhizobium. Although the forest floor bacteria came from the topsoil at the same sampling site, the bacterial community structure had changed significantly. This study indicated that tree species drive the change of soil bacterial community by changing the soil C/N ratio, which may provide a new perspective for maintaining the stability of regional ecosystem structure.
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Affiliation(s)
- Hanjiang Nie
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100038, China; Department of Hydraulic Engineering, Tsinghua University, Beijing 100084, China
| | - Tianling Qin
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100038, China.
| | - Denghua Yan
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100038, China.
| | - Xizhi Lv
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100038, China; Key Laboratory of the Loess Plateau Soil Erosion and Water Loss Process and Control of Ministry of Water Resources, Yellow River Institute of Hydraulic Research, Zhengzhou 450003, China
| | - Jianwei Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
| | - Yinghou Huang
- College of Hydrology and Water Resources, Hohai University, Nanjing, Jiangsu 210098, China
| | - Zhenyu Lv
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100038, China; Department of Hydraulic Engineering, Tsinghua University, Beijing 100084, China
| | - Shanshan Liu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
| | - Fang Liu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
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Ito N, Mori N, Miyashita NT. Rhizospheric bacterial community structure of Triticum and Aegilops revealed by pyrosequencing analysis of the 16S rRNA gene: dominance of the A genome over the B and D genomes. Genes Genet Syst 2020; 95:249-268. [PMID: 33298661 DOI: 10.1266/ggs.20-00006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
This study examined the relationship between host plant and rhizospheric bacterial community structure, including composition and diversity, in Triticum and Aegilops species (12 and two accessions, respectively) as well as three closely related species, barley, rye and oat (four accessions), to explore the possibility that wheat root and rhizosphere interaction can be utilized for wheat breeding and biotechnology in the future. For this purpose, DNA was isolated from rhizospheric soil samples and one control non-rhizospheric soil sample, and the 16S rRNA gene region was amplified and subjected to DNA pyrosequencing. A total of 132,888 amplicons were analyzed. Bacterial composition at the phylum level was similar among the 18 rhizospheric samples; however, the proportion of Acidobacteria was much lower in these samples than in the control non-rhizospheric soil sample, indicating that rhizospheres influenced the bacterial composition even at the higher taxonomic level. Across host plant genome types (three levels of ploidy and three major genomes, A, B and D), there was no detectable difference in phylum composition or species diversity. Estimated bacterial species diversity was higher in the control soil sample than in plant rhizospheric soils, implying that bacterial species diversity was reduced in rhizospheres. A PCoA plot and UPGMA dendrogram based on the bacterial species composition showed that control soil was distantly located from the plant rhizospheric samples and that Triticum, Aegilops and related species were well separated. PERMANOVA analysis detected statistically significant differentiation among these four groups. Clustering of Triticum species suggested that the A genome was dominant over the B and D genomes, with respect to the influence on rhizospheric bacterial species composition. Although the cause was not investigated in this study, these results clearly indicated that the genetic constitution of the plant host exerted a strong influence on rhizospheric bacterial community structure.
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Affiliation(s)
- Natsumi Ito
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University
| | - Naoki Mori
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kobe University
| | - Naohiko T Miyashita
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University
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6
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Chua CY, Wong CMVL. Effects of simulated warming on bacterial diversity and abundance in tropical soils from East Malaysia using open top chambers. Can J Microbiol 2020; 67:64-74. [PMID: 33084348 DOI: 10.1139/cjm-2019-0461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The effects of global warming are increasingly evident, where global surface temperatures and atmospheric concentration of carbon dioxide have increased in past decades. Given the role of terrestrial bacteria in various ecological functions, it is important to understand how terrestrial bacteria would respond towards higher environmental temperatures. This study aims to determine soil bacterial diversity in the tropics and their response towards in situ warming using an open-top chamber (OTC). OTCs were set up in areas exposed to sunlight throughout the year in the tropical region in Malaysia. Soil samples were collected every 3 months to monitor changes in bacterial diversity using V3-V4 16S rDNA amplicon sequencing inside the OTCs (treatment plots) and outside the OTCs (control plots). After 12 months of simulated warming, an average increase of 0.81 to 1.15 °C was recorded in treatment plots. Significant changes in the relative abundance of bacterial phyla such as Bacteroidetes and Chloroflexi were reported. Increases in the relative abundance of Actinobacteria were also observed in treatment plots after 12 months. Substantial changes were observed at the genus level, where most bacterial genera decreased in relative abundance after 12 months. This study demonstrated that warming can alter soil bacteria in tropical soils from Kota Kinabalu.
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Affiliation(s)
- Chuen Yang Chua
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.,Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Clemente Michael Vui Ling Wong
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.,Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
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7
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Harnvoravongchai P, Singwisut R, Ounjai P, Aroonnual A, Kosiyachinda P, Janvilisri T, Chankhamhaengdecha S. Isolation and characterization of thermophilic cellulose and hemicellulose degrading bacterium, Thermoanaerobacterium sp. R63 from tropical dry deciduous forest soil. PLoS One 2020; 15:e0236518. [PMID: 32702033 PMCID: PMC7377481 DOI: 10.1371/journal.pone.0236518] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/07/2020] [Indexed: 12/31/2022] Open
Abstract
Thermophilic microorganisms and their enzymes have been utilized in various industrial applications. In this work, we isolated and characterized thermophilic anaerobic bacteria with the cellulose and hemicellulose degrading activities from a tropical dry deciduous forest in northern Thailand. Out of 502 isolated thermophilic anaerobic soil bacteria, 6 isolates, identified as Thermoanaerobacterium sp., displayed an ability to utilize a wide range of oligosaccharides and lignocellulosic substrates. The isolates exhibited significant cellulase and xylanase activities at high temperature (65°C). Among all isolates, Thermoanaerobacterium sp. strain R63 exhibited remarkable hydrolytic properties with the highest cellulase and xylanase activities at 1.15 U/mg and 6.17 U/mg, respectively. Extracellular extract of Thermoanaerobacterium sp. strain R63 was thermostable with an optimal temperature at 65°C and could exhibit enzymatic activities on pH range 5.0-9.0. Our findings suggest promising applications of these thermoanaerobic bacteria and their potent enzymes for industrial purposes.
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Affiliation(s)
| | - Ratiyakorn Singwisut
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Amornrat Aroonnual
- Department of Tropical Nutrition and Food Science, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Pahol Kosiyachinda
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
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8
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Manpoong C, De Mandal S, Bangaruswamy DK, Perumal RC, Benny J, Beena P, Ghosh A, Kumar NS, Tripathi SK. Linking rhizosphere soil biochemical and microbial community characteristics across different land use systems in mountainous region in Northeast India. Meta Gene 2020. [DOI: 10.1016/j.mgene.2019.100625] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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9
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Chernov TI, Zhelezova AD, Tkhakakhova AK, Bgazhba NA, Zverev AO. Microbiomes of Virgin Soils of Southern Vietnam Tropical Forests. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719040040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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10
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Xia X, Zhang P, He L, Gao X, Li W, Zhou Y, Li Z, Li H, Yang L. Effects of tillage managements and maize straw returning on soil microbiome using 16S rDNA sequencing. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:765-777. [PMID: 30912294 DOI: 10.1111/jipb.12802] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 03/12/2019] [Indexed: 05/07/2023]
Abstract
Agricultural practices could affect bacterial diversity and community structure by altering soil physical and chemical properties. Straw returning and tillage practices are widely used in agriculture, however, the effects of these agricultural practices on microbiomes are still unclear. In the present study, we compared the 18 bacterial communities of soil with different straw returning and tillage treatment combinations. The V3-V4 regions of the 16S ribosomal RNA were amplified and analyzed by high-throughput sequencing technology. The results showed that the bacterial communities were consistently dominated by Acidobacteria, Proteobacteria, Actinobacteria, and Chloroflexi. Short-term straw returning and tillage practices significantly altered the diversity, relative abundance and functions of the soil microbiome. Soil subjected to rotary tillage and straw returning (RTS) combination possessed the highest bacterial diversity and lowest ratio of G+/G- bacteria, indicating that RTS could be an efficient integrated management system to improve microbiome in the short term. Double verifications based on relative abundance and network analysis, revealed close relationships of Mycobacterium and Methylibium with RTS, indicating they could serve as biomarkers for RTS. Investigating microbial changes under different agricultural practices will provide valuable foundations for land sustainable utilization and increase crop yields.
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Affiliation(s)
- Xinyao Xia
- Agricultural Big-Data Research Center, College of Plant Protection, Shandong Agricultural University, Taian, 271018, China
| | - Piaopiao Zhang
- Department of Clinical, Taishan Medical University, Taian, 271016, China
| | - Linlin He
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Xingxing Gao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Weijun Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Yuanyuan Zhou
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Zongxin Li
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Hui Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Long Yang
- Agricultural Big-Data Research Center, College of Plant Protection, Shandong Agricultural University, Taian, 271018, China
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11
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Goss-Souza D, Mendes LW, Borges CD, Baretta D, Tsai SM, Rodrigues JLM. Soil microbial community dynamics and assembly under long-term land use change. FEMS Microbiol Ecol 2017; 93:4102335. [DOI: 10.1093/femsec/fix109] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/31/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Dennis Goss-Souza
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400–970, Brazil
- Applied Ecology Graduate Program, Luiz de Queiroz School of Agriculture, University of São Paulo, Piracicaba, SP, 13418–900, Brazil
- Department of Land, Air and Water Resources, University of California – Davis, Davis, CA 95616, USA
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400–970, Brazil
| | - Clovis Daniel Borges
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400–970, Brazil
- Applied Ecology Graduate Program, Luiz de Queiroz School of Agriculture, University of São Paulo, Piracicaba, SP, 13418–900, Brazil
| | - Dilmar Baretta
- Department of Soils and Sustainability, Santa Catarina State University, Chapecó, SC, 89815-630, Brazil
| | - Siu Mui Tsai
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400–970, Brazil
| | - Jorge L. M. Rodrigues
- Department of Land, Air and Water Resources, University of California – Davis, Davis, CA 95616, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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12
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Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach. PLoS One 2016. [PMID: 27907121 DOI: 10.1371/journal.pone.0167405,] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity. Therefore, four plant formation types at two distinct sites were studied. These formations represent different stages in a potential chronosequence. Soil cores, according to a given sampling procedure, were collected to assess microbial diversity using a metagenomic approach, and to characterise the physico-chemical parameters. A botanical inventory was also performed. Our results indicated that microbial richness, composition and abundance were linked to the plant cover type and the dominant plant species. Furthermore, a large proportion of Ascomycota phylum (fungi), mostly in non-rainforest formations, and Planctomycetes phylum (bacteria) in all formations were observed. Interestingly, such patterns could be indicators of past disturbances that occurred on different time scales. Furthermore, the bacteria and fungi were influenced by diverse edaphic parameters as well as by the interplay between these two soil communities. Another striking finding was the existence of a site effect. Differences in microbial communities between geographical locations may be explained by dispersal limitation in the context of the biogeographical island theory. In conclusion, each plant formation at each site possesses is own microbial community resulting from multiple interactions between abiotic and biotic factors.
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13
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Gourmelon V, Maggia L, Powell JR, Gigante S, Hortal S, Gueunier C, Letellier K, Carriconde F. Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach. PLoS One 2016; 11:e0167405. [PMID: 27907121 PMCID: PMC5131939 DOI: 10.1371/journal.pone.0167405] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/14/2016] [Indexed: 11/30/2022] Open
Abstract
Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity. Therefore, four plant formation types at two distinct sites were studied. These formations represent different stages in a potential chronosequence. Soil cores, according to a given sampling procedure, were collected to assess microbial diversity using a metagenomic approach, and to characterise the physico-chemical parameters. A botanical inventory was also performed. Our results indicated that microbial richness, composition and abundance were linked to the plant cover type and the dominant plant species. Furthermore, a large proportion of Ascomycota phylum (fungi), mostly in non-rainforest formations, and Planctomycetes phylum (bacteria) in all formations were observed. Interestingly, such patterns could be indicators of past disturbances that occurred on different time scales. Furthermore, the bacteria and fungi were influenced by diverse edaphic parameters as well as by the interplay between these two soil communities. Another striking finding was the existence of a site effect. Differences in microbial communities between geographical locations may be explained by dispersal limitation in the context of the biogeographical island theory. In conclusion, each plant formation at each site possesses is own microbial community resulting from multiple interactions between abiotic and biotic factors.
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Affiliation(s)
- Véronique Gourmelon
- Institut Agronomique néo-Calédonien (IAC), Axe 2 "Diversités biologique et fonctionnelle des écosystèmes terrestres", Nouméa, New Caledonia
| | - Laurent Maggia
- Institut Agronomique néo-Calédonien (IAC), Axe 2 "Diversités biologique et fonctionnelle des écosystèmes terrestres", Nouméa, New Caledonia.,CIRAD, UMR AGAP, Nouméa, New Caledonia
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Sarah Gigante
- Institut Agronomique néo-Calédonien (IAC), Axe 2 "Diversités biologique et fonctionnelle des écosystèmes terrestres", Nouméa, New Caledonia
| | - Sara Hortal
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Claire Gueunier
- Société Le Nickel (SLN) - Groupe ERAMET, Département Environnement, Nouméa, New Caledonia
| | - Kelly Letellier
- Institut Agronomique néo-Calédonien (IAC), Axe 2 "Diversités biologique et fonctionnelle des écosystèmes terrestres", Nouméa, New Caledonia
| | - Fabian Carriconde
- Institut Agronomique néo-Calédonien (IAC), Axe 2 "Diversités biologique et fonctionnelle des écosystèmes terrestres", Nouméa, New Caledonia
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14
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Screening for Urease-Producing Bacteria from Limestone Caves of Sarawak. BORNEO JOURNAL OF RESOURCE SCIENCE AND TECHNOLOGY 2016. [DOI: 10.33736/bjrst.213.2016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Urease is a key enzyme in the chemical reaction of microorganism and has been found to be associated withcalcification, which is essential in microbially induced calcite precipitation (MICP) process. Three bacterialisolates (designated as LPB19, TSB31 and TSB12) were among twenty-eight bacteria that were isolated fromsamples collected from Sarawak limestone caves using the enrichment culture technique. Isolates LPB19, TSB31and TSB12 were selected based on their quick urease production when compared to other isolates. Phenotypiccharacteristics indicate all three bacterial strains are gram-positive, rod-shaped, motile, catalase and oxidasepositive. Urease activity of the bacterial isolates were measured through changes in conductivity in the absence ofcalcium ions. The bacterial isolates (LPB19, TSB12 and TSB31) showed urease activity of 16.14, 12.45 and 11.41mM urea hydrolysed/min respectively. The current work suggested that these isolates serves as constitutiveproducers of urease, potentially useful in inducing calcite precipitates.
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15
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Miyashita NT. Contrasting soil bacterial community structure between the phyla Acidobacteria and Proteobacteria in tropical Southeast Asian and temperate Japanese forests. Genes Genet Syst 2016; 90:61-77. [PMID: 26399766 DOI: 10.1266/ggs.90.61] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Soil bacterial community structures of six dominant phyla (Acidobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes, Bacteroidetes and Actinobacteria) and unclassified bacteria detected in tropical Sarawakian and temperate Japanese forests were compared based on 16S rRNA gene sequence variation. The class composition in each phylum was similar among the studied forests; however, significant heterogeneities of class frequencies were detected. Acidobacteria and Proteobacteria were the most dominant phyla in all six forests, but differed in the level of bacterial species diversity, pattern of species occurrence and association pattern of species composition with physicochemical properties in soil. Species diversity among Acidobacteria was approximately half that among Proteobacteria, based on the number of clusters and the Chao1 index, even though a similar number of sequence reads were obtained for these two phyla. In contrast, species diversity within Planctomycetes and Bacteroidetes was nearly as high as within Acidobacteria, despite many fewer sequence reads. The density of species (the number of sequence reads per cluster) correlated negatively with species diversity, and species density within Acidobacteria was approximately twice that within Proteobacteria. Although the percentage of forest-specific species was high for all bacterial groups, sampling site-specific species varied among bacterial groups, indicating limited inter-forest migration and differential movement of bacteria in forest soil. For five of the seven bacterial groups, including Acidobacteria, soil pH appeared to strongly influence species composition, but this association was not observed for Proteobacterial species. Topology of UPGMA trees and pattern of NMDS plots among the forests differed among the bacterial groups, suggesting that each bacterial group has adapted and evolved independently in each forest.
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Affiliation(s)
- Naohiko T Miyashita
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University
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16
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Tripathi BM, Song W, Slik JWF, Sukri RS, Jaafar S, Dong K, Adams JM. Distinctive Tropical Forest Variants Have Unique Soil Microbial Communities, But Not Always Low Microbial Diversity. Front Microbiol 2016; 7:376. [PMID: 27092105 PMCID: PMC4820907 DOI: 10.3389/fmicb.2016.00376] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 03/08/2016] [Indexed: 11/21/2022] Open
Abstract
There has been little study of whether different variants of tropical rainforest have distinct soil microbial communities and levels of diversity. We compared bacterial and fungal community composition and diversity between primary mixed dipterocarp, secondary mixed dipterocarp, white sand heath, inland heath, and peat swamp forests in Brunei Darussalam, Northwest Borneo by analyzing Illumina Miseq sequence data of 16S rRNA gene and ITS1 region. We hypothesized that white sand heath, inland heath and peat swamp forests would show lower microbial diversity and relatively distinct microbial communities (compared to MDF primary and secondary forests) due to their distinctive environments. We found that soil properties together with bacterial and fungal communities varied significantly between forest types. Alpha and beta-diversity of bacteria was highest in secondary dipterocarp and white sand heath forests. Also, bacterial alpha diversity was strongly structured by pH, adding another instance of this widespread pattern in nature. The alpha diversity of fungi was equally high in all forest types except peat swamp forest, although fungal beta-diversity was highest in primary and secondary mixed dipterocarp forests. The relative abundance of ectomycorrhizal (EcM) fungi varied significantly between forest types, with highest relative abundance observed in MDF primary forest. Overall, our results suggest that the soil bacterial and fungal communities in these forest types are to a certain extent predictable and structured by soil properties, but that diversity is not determined by how distinctive the conditions are. This contrasts with the diversity patterns seen in rainforest trees, where distinctive soil conditions have consistently lower tree diversity.
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Affiliation(s)
- Binu M Tripathi
- Department of Biological Science, College of Natural Sciences, Seoul National University Seoul, South Korea
| | - Woojin Song
- Department of Biological Science, College of Natural Sciences, Seoul National UniversitySeoul, South Korea; Seoul ZooSeoul, South Korea
| | - J W F Slik
- Faculty of Science, Universiti Brunei Darussalam Gadong, Brunei Darussalam
| | - Rahayu S Sukri
- Faculty of Science, Universiti Brunei Darussalam Gadong, Brunei Darussalam
| | - Salwana Jaafar
- Faculty of Science, Universiti Brunei Darussalam Gadong, Brunei Darussalam
| | - Ke Dong
- Department of Biological Science, College of Natural Sciences, Seoul National University Seoul, South Korea
| | - Jonathan M Adams
- Department of Biological Science, College of Natural Sciences, Seoul National University Seoul, South Korea
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Living with detergents: pyrosequencing-based assessment of bacterial community structures in soils subjected for decades to contamination by detergents. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0969-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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18
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Kim YE, Yoon H, Kim M, Nam YJ, Kim H, Seo Y, Lee GM, Ja Kim Y, Kong WS, Kim JG, Seu YB. Metagenomic analysis of bacterial communities on Dokdo Island. J GEN APPL MICROBIOL 2014; 60:65-74. [DOI: 10.2323/jgam.60.65] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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