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Cui C, Song Y, Mao D, Cao Y, Qiu B, Gui P, Wang H, Zhao X, Huang Z, Sun L, Zhong Z. Predicting the Postmortem Interval Based on Gravesoil Microbiome Data and a Random Forest Model. Microorganisms 2022; 11:microorganisms11010056. [PMID: 36677348 PMCID: PMC9860995 DOI: 10.3390/microorganisms11010056] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/11/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
The estimation of a postmortem interval (PMI) is particularly important for forensic investigations. The aim of this study was to assess the succession of bacterial communities associated with the decomposition of mouse cadavers and determine the most important biomarker taxa for estimating PMIs. High-throughput sequencing was used to investigate the bacterial communities of gravesoil samples with different PMIs, and a random forest model was used to identify biomarker taxa. Redundancy analysis was used to determine the significance of environmental factors that were related to bacterial communities. Our data showed that the relative abundance of Proteobacteria, Bacteroidetes and Firmicutes showed an increasing trend during decomposition, but that of Acidobacteria, Actinobacteria and Chloroflexi decreased. At the genus level, Pseudomonas was the most abundant bacterial group, showing a trend similar to that of Proteobacteria. Soil temperature, total nitrogen, NH4+-N and NO3--N levels were significantly related to the relative abundance of bacterial communities. Random forest models could predict PMIs with a mean absolute error of 1.27 days within 36 days of decomposition and identified 18 important biomarker taxa, such as Sphingobacterium, Solirubrobacter and Pseudomonas. Our results highlighted that microbiome data combined with machine learning algorithms could provide accurate models for predicting PMIs in forensic science and provide a better understanding of decomposition processes.
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Affiliation(s)
- Chunhong Cui
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- College of Resource and Environment, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Song
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Dongmei Mao
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yajun Cao
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bowen Qiu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Gui
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xingchun Zhao
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Beijing 100038, China
- Correspondence: (X.Z.); (Z.H.); (L.S.)
| | - Zhi Huang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (X.Z.); (Z.H.); (L.S.)
| | - Liqiong Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (X.Z.); (Z.H.); (L.S.)
| | - Zengtao Zhong
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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2
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Kumaishi K, Usui E, Suzuki K, Kobori S, Sato T, Toda Y, Takanashi H, Shinozaki S, Noda M, Takakura A, Matsumoto K, Yamasaki Y, Tsujimoto H, Iwata H, Ichihashi Y. High throughput method of 16S rRNA gene sequencing library preparation for plant root microbial community profiling. Sci Rep 2022; 12:19289. [PMID: 36369356 PMCID: PMC9652414 DOI: 10.1038/s41598-022-23943-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022] Open
Abstract
Microbiota are a major component of agroecosystems. Root microbiota, which inhabit the inside and surface of plant roots, play a significant role in plant growth and health. As next-generation sequencing technology allows the capture of microbial profiles without culturing the microbes, profiling of plant microbiota has become a staple tool in plant science and agriculture. Here, we have increased sample handling efficiency in a two-step PCR amplification protocol for 16S rRNA gene sequencing of plant root microbiota, improving DNA extraction using AMPure XP magnetic beads and PCR purification using exonuclease. These modifications reduce sample handling and capture microbial diversity comparable to that obtained by the manual method. We found a buffer with AMPure XP magnetic beads enabled efficient extraction of microbial DNA directly from plant roots. We also demonstrated that purification using exonuclease before the second PCR step enabled the capture of higher degrees of microbial diversity, thus allowing for the detection of minor bacteria compared with the purification using magnetic beads in this step. In addition, our method generated comparable microbiome profile data in plant roots and soils to that of using common commercially available DNA extraction kits, such as DNeasy PowerSoil Pro Kit and FastDNA SPIN Kit for Soil. Our method offers a simple and high-throughput option for maintaining the quality of plant root microbial community profiling.
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Affiliation(s)
- Kie Kumaishi
- grid.509462.cRIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074 Japan
| | - Erika Usui
- grid.509462.cRIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074 Japan
| | - Kenta Suzuki
- grid.509462.cRIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074 Japan
| | - Shungo Kobori
- grid.509462.cRIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074 Japan
| | - Takumi Sato
- grid.509462.cRIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074 Japan
| | - Yusuke Toda
- grid.26999.3d0000 0001 2151 536XGraduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657 Japan
| | - Hideki Takanashi
- grid.26999.3d0000 0001 2151 536XGraduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657 Japan
| | - Satoshi Shinozaki
- MAYEKAWA Research Institute Co., LTD, Koto-Ku, Tokyo, 135-8482 Japan
| | - Munehiro Noda
- MAYEKAWA Research Institute Co., LTD, Koto-Ku, Tokyo, 135-8482 Japan
| | - Akiko Takakura
- MAYEKAWA Research Institute Co., LTD, Koto-Ku, Tokyo, 135-8482 Japan
| | - Kayoko Matsumoto
- MAYEKAWA Research Institute Co., LTD, Koto-Ku, Tokyo, 135-8482 Japan
| | - Yuji Yamasaki
- grid.265107.70000 0001 0663 5064Arid Land Research Center, Tottori University, Tottori, 680-0001 Japan
| | - Hisashi Tsujimoto
- grid.265107.70000 0001 0663 5064Arid Land Research Center, Tottori University, Tottori, 680-0001 Japan
| | - Hiroyoshi Iwata
- grid.26999.3d0000 0001 2151 536XGraduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657 Japan
| | - Yasunori Ichihashi
- grid.509462.cRIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074 Japan
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3
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Zeng Q, Man X, Lebreton A, Dai Y, Martin FM. The bacterial and fungal microbiomes of ectomycorrhizal roots from stone oaks and Yunnan pines in the subtropical forests of the Ailao Mountains of Yunnan. Front Microbiol 2022; 13:916337. [PMID: 35966686 PMCID: PMC9372452 DOI: 10.3389/fmicb.2022.916337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/11/2022] [Indexed: 12/02/2022] Open
Abstract
Ectomycorrhizal (ECM) symbioses play an important role in tree biology and forest ecology. However, little is known on the composition of bacterial and fungal communities associated to ECM roots. In the present study, we surveyed the bacterial and fungal microbiome of ECM roots from stone oaks (Lithocarpus spp.) and Yunnan pines (Pinus yunnanensis) in the subtropical forests of the Ailao Mountains (Yunnan, China). The bacterial community was dominated by species pertaining to Rhizobiales and Acidobacteriales, whereas the fungal community was mainly composed of species belonging to the Russulales and Thelephorales. While the bacterial microbiome hosted by ECM roots from stone oaks and Yunnan pines was very similar, the mycobiome of these host trees was strikingly distinct. The microbial networks for bacterial and fungal communities showed a higher complexity in Lithocarpus ECM roots compared to Pinus ECM roots, but their modularity was higher in Pinus ECM roots. Seasonality also significantly influenced the fungal diversity and their co-occurrence network complexity. Our findings thus suggest that the community structure of fungi establishing and colonizing ECM roots can be influenced by the local soil/host tree environment and seasonality. These results expand our knowledge of the ECM root microbiome and its diversity in subtropical forest ecosystems.
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Affiliation(s)
- Qingchao Zeng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Xiaowu Man
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Annie Lebreton
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, Champenoux, France
| | - Yucheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
- *Correspondence: Yucheng Dai,
| | - Francis M. Martin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, Champenoux, France
- Francis M. Martin,
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4
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Generalists and Specialists Determine the Trend and Rate of Soil Fungal Distance Decay of Similarity in a 20-ha Subtropical Forest. FORESTS 2022. [DOI: 10.3390/f13081188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fungi are an important component of microbial communities that serve a variety of important roles in nutrient cycling and are essential for plant nutrient uptake in forest soils. Distance decay of similarity (DDS) is one of the few ubiquitous phenomena in community ecology. However, the contribution of specialist and generalist fungal species in shaping DDS remains poorly investigated. Through removing operational taxonomic units (OTU) with low or high frequencies, we rigorously quantified the impact of specialists or generalists on the change in slope, initial similarity, and halving distance of DDS of undefined saprotroph, plant mutualist, and plant putative pathogen communities in a 20-ha subtropical evergreen forest plot in Yunnan Province, Southwest China. We hypothesized that (1) the soil fungal co-occurrence networks are different between the three fungal guilds; (2) specialists and generalists contribute to the spatial turnover and nestedness of beta diversity, respectively; and (3) the removal of specialists or generalists will have opposite effects on the change of slope, initial similarity, and halving distance of DDS. Co-occurrence network analysis showed that the undefined saprotroph network had a much more complicated structure than mutualist and pathogen networks. Ascomycota and Basidiomycota were the two most abundant phyla in soil fungal communities. We found that partly in line with our expectations, the change in initial similarity increased and decreased when removing specialists and generalists, respectively, but there was always one exception guild of out of the three communities for the change in slope and halving distance. We identified that such change was mainly due to the change in turnover and nestedness of beta diversity. Furthermore, the results show that species turnover rather than species nestedness drove fungal beta diversity across functional guilds for both specialists and generalists.
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5
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Zeng Q, Lebreton A, Man X, Jia L, Wang G, Gong S, Buée M, Wu G, Dai Y, Yang Z, Martin FM. Ecological Drivers of the Soil Microbial Diversity and Composition in Primary Old-Growth Forest and Secondary Woodland in a Subtropical Evergreen Broad-Leaved Forest Biome in the Ailao Mountains, China. Front Microbiol 2022; 13:908257. [PMID: 35770159 PMCID: PMC9234548 DOI: 10.3389/fmicb.2022.908257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/20/2022] [Indexed: 12/13/2022] Open
Abstract
Replacement of primary old-growth forests by secondary woodlands in threatened subtropical biomes drives important changes at the level of the overstory, understory and forest floor, but the impact on belowground microbial biodiversity is yet poorly documented. In the present study, we surveyed by metabarcoding sequencing, the diversity and composition of soil bacteria and fungi in the old-growth forest, dominated by stone oaks (Lithocarpus spp.) and in the secondary Yunnan pine woodland of an iconic site for biodiversity research, the Ailaoshan National Nature Reserve (Ailao Mountains, Yunnan province, China). We assessed the effect of forest replacement and other environmental factors, including soil horizons, soil physicochemical characteristics and seasonality (monsoon vs. dry seasons). We showed that tree composition and variation in soil properties were major drivers for both bacterial and fungal communities, with a significant influence from seasonality. Ectomycorrhizal Operational Taxonomic Units (OTUs) dominated the functional fungal guilds. Species richness and diversity of the bacterial and fungal communities were higher in the pine woodland compared to the primary Lithocarpus forest, although prominent OTUs were different. The slightly lower complexity of the microbiome in the primary forest stands likely resulted from environmental filtering under relatively stable conditions over centuries, when compared to the secondary pine woodlands. In the old-growth forest, we found a higher number of species, but that communities were homogeneously distributed, whereas in the pine woodlands, there is a slightly lower number of species present but the communities are heterogeneously distributed. The present surveys of the bacterial and fungal diversity will serve as references in future studies aiming to assess the impact of the climate change on soil microbial diversity in both old-growth forests and secondary woodlands in Ailaoshan.
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Affiliation(s)
- Qingchao Zeng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Annie Lebreton
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE-GrandEst-Nancy, Université de Lorraine, Champenoux, France
| | - Xiaowu Man
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Liukun Jia
- Chinese Academy of Sciences Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Kunming, China
| | - Gengshen Wang
- Chinese Academy of Sciences Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Kunming, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, China
| | - Sai Gong
- Chinese Academy of Sciences Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Kunming, China
| | - Marc Buée
- INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE-GrandEst-Nancy, Université de Lorraine, Champenoux, France
| | - Gang Wu
- Chinese Academy of Sciences Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Kunming, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, China
| | - Yucheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Zhuliang Yang
- Chinese Academy of Sciences Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Kunming, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, China
| | - Francis M. Martin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE-GrandEst-Nancy, Université de Lorraine, Champenoux, France
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6
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Zeeshan M, Wenjun Z, Chuansheng W, Yan L, Azeez PA, Qinghai S, Yuntong L, Yiping Z, Zhiyun L, Liqing S. Soil heterotrophic respiration in response to rising temperature and moisture along an altitudinal gradient in a subtropical forest ecosystem, Southwest China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151643. [PMID: 34780839 DOI: 10.1016/j.scitotenv.2021.151643] [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: 07/27/2021] [Revised: 10/20/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Globally, one-third of the terrestrial carbon (C) is stored in tropical soils. The warming predicted for this century is expected to increase microbial decomposition in soil and escalate climate change potential by releasing more carbon dioxide (CO2) into the atmosphere. Understanding the response of soils to warming is a key challenge in predicting future climate change trajectories. Here we examined the combined effect of soil temperature (Ts) and soil water content (VWC) on soil heterotrophic respiration (Rsh) and its temperature sensitivity across different altitudes (2400, 1900, and 1450 m ASL) in the Ailaoshan subtropical forest ecosystem, Southwest China. Along the elevation gradient, soil C stocks in the top 10 cm soil layer increased significantly from 10.7 g/ kg at 1480 m ASL to 283.1 g/ kg at 2480 m ASL. Soil cores from various elevations were translocated to the same, and lower elevations and Rsh from those cores were measured every month from February 2010 to January 2014. Temperature sensitivity (Q10) of Rsh for the period was highest at the highest (H) elevation (Q10 = 5.3), decreased significantly towards the middle (M, Q10 = 3.1) and low (L, Q10 = 1.2) elevation. Q10 at M and L elevation did not differ between the place of origin and translocated cores. For the cores within each elevation, Q10 did not vary across the years. Our models suggest that Rsh increased significantly in response to an increase in Ts at each elevation under an intermediate VWC. Hence, the rate of emission was higher in lower elevations due to a higher Ts range. Our findings highlight that the predicted warming over the 21st century will have the greatest impact of Ts on Rsh, especially on the soils at the highest elevations, and will lead towards positive feedback to the climate system.
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Affiliation(s)
- Mohd Zeeshan
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
| | - Zhou Wenjun
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China; Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China.
| | - Wu Chuansheng
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Fuyang Normal University, Fuyang, China, 100 Qinghe Rd, 236037 Fuyang, Anhui, China.
| | - Lin Yan
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720-3114, USA
| | - P A Azeez
- Visiting Faculty, Department of Environmental Management, Bharathidasan University, Trichy 620024, Tamil Nadu, India
| | - Song Qinghai
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China; Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
| | - Liu Yuntong
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China; Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
| | - Zhang Yiping
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China; Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
| | - Lu Zhiyun
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China; Ailaoshan Station for Subtropical Forest Ecosystem Studies, Jingdong, Yunnan 676209, China
| | - Sha Liqing
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China; Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
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7
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The effect of snow damage on self-organization in a primary subtropical evergreen broadleaved forest in Southwest China. ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2021.101482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Influence of rhizosphere activity on litter decomposition in subtropical forest: implications of estimating soil organic matter contributions to soil respiration. JOURNAL OF TROPICAL ECOLOGY 2022. [DOI: 10.1017/s0266467422000013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Abstract
Litter decomposition plays an important role in the carbon cycle and is affected by many factors in forest ecosystems. This study aimed to quantify the rhizosphere priming effect on litter decomposition in subtropical forest southwestern China. A litter decomposition experiment including control and trenching treatments was conducted using the litter bag method, and the litter decomposition rate was calculated by litter dry mass loss. Trenching did not change soil temperature, but increased the soil water content by 14.5%. In this study, the interaction of soil temperature and soil water content controlled the litter decomposition rate, and explained 87.4 and 85.5% of the variation in litter decomposition in the control and trenching treatments, respectively. Considering changes in soil environmental factors due to trenching, the litter decomposition rates were corrected by regression models. After correction, the litter decomposition rates of the control and trenching treatments were 32.47 ± 3.15 and 25.71 ± 2.72% year–1, respectively, in the 2-year period. Rhizosphere activity significantly primed litter decomposition by 26.3%. Our study suggested a priming effect of rhizosphere activity on litter decomposition in the subtropical forest. Combining previous interaction effect results, we estimated the contributions of total soil organic matter (SOM) decomposition, total litter decomposition, and root respiration to soil respiration in the subtropical forest, and our new method of estimating the components of soil respiration provided basic theory for SOM decomposition research.
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Yu L, Zhu J, Ji H, Bai X, Lin Y, Zhang Y, Sha L, Liu Y, Song Q, Dörsch P, Mulder J, Zhou W. Topography-related controls on N 2O emission and CH 4 uptake in a tropical rainforest catchment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 775:145616. [PMID: 33631582 DOI: 10.1016/j.scitotenv.2021.145616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/29/2021] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
Forest soils in the warm-humid tropics significantly contribute to the regional greenhouse gas (GHG) budgets. However, spatial heterogeneity of GHG fluxes is often overlooked. Here, we present a study of N2O and CH4 fluxes over 1.5 years, along a topographic gradient in a rainforest catchment in Xishuangbanna, SW China. From the upper hillslope to the foot of the hillslope, and further to the flat groundwater discharge zone, we observed a decrease of N2O emission associated with an increase of soil water-filled-pore-space (WFPS), which we tentatively attribute to more complete denitrification to N2 at larger WFPS. In the well-drained soils on the hillslope, denitrification at anaerobic microsites or under transient water-saturation was the potential N2O source. Negative CH4 fluxes across the catchment indicated a net soil CH4 sink. As the oxidation of atmospheric CH4 is diffusion-limited, soil CH4 consumption rates were negatively related to WFPS, reflecting the topographic control. Our observations also suggest that during dry seasons N2O emission was significantly dampened (<10 μg N2O-N m-2 h-1) and CH4 uptake was strongly enhanced (83 μg CH4-C m-2 h-1) relative to wet seasons (17 μg N2O-N m-2 h-1 and 56 μg CH4-C m-2 h-1). In a post-drought period, several rain episodes induced exceptionally high N2O emissions (450 μg N2O-N m-2 h-1) in the groundwater discharge zone, likely driven by flushing of labile organic carbon accumulated during drought. Considering the global warming potential associated with both GHGs, we found that N2O emissions largely offset the C sink contributed by CH4 uptake in soils (more significant in the groundwater discharge zone). Our study illustrates important topographic controls on N2O and CH4 fluxes in forest soils. With projected climate change in the tropics, weather extremes may interact with these controls in regulating forest GHG fluxes, which should be accounted for in future studies.
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Affiliation(s)
- Longfei Yu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303 Mengla, Yunnan, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, 666303 Xishuangbanna, Yunnan, China; Institute of Groundwater and Earth Sciences, Jinan University, 510632 Guangzhou, China; Laboratory for Air Pollution & Environmental Technology, Empa, Swiss Federal Laboratories for Materials Science and Technology, Ueberlandstr. 129, CH-8600 Duebendorf, Switzerland
| | - Jing Zhu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303 Mengla, Yunnan, China; Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, 54004 Guilin, China.
| | - Hongli Ji
- Lushan Botanical Garden, Jiangxi Province, Chinese Academy of Sciences, 332900 Jiujiang, China
| | - Xiaolong Bai
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303 Mengla, Yunnan, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, 666303 Xishuangbanna, Yunnan, China; University of Chinese Academy of Sciences, 100039 Beijing, China
| | - Youxing Lin
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303 Mengla, Yunnan, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, 666303 Xishuangbanna, Yunnan, China; University of Chinese Academy of Sciences, 100039 Beijing, China
| | - Yiping Zhang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303 Mengla, Yunnan, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, 666303 Xishuangbanna, Yunnan, China; University of Chinese Academy of Sciences, 100039 Beijing, China
| | - Liqing Sha
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303 Mengla, Yunnan, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, 666303 Xishuangbanna, Yunnan, China; University of Chinese Academy of Sciences, 100039 Beijing, China
| | - Yuntong Liu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303 Mengla, Yunnan, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, 666303 Xishuangbanna, Yunnan, China; University of Chinese Academy of Sciences, 100039 Beijing, China
| | - Qinghai Song
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303 Mengla, Yunnan, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, 666303 Xishuangbanna, Yunnan, China; University of Chinese Academy of Sciences, 100039 Beijing, China
| | - Peter Dörsch
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Postbox 5003, N-1432 Aas, Norway
| | - Jan Mulder
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Postbox 5003, N-1432 Aas, Norway
| | - Wenjun Zhou
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303 Mengla, Yunnan, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, 666303 Xishuangbanna, Yunnan, China; University of Chinese Academy of Sciences, 100039 Beijing, China.
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10
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Xu R, Sun X, Häggblom MM, Dong Y, Zhang M, Yang Z, Xiao E, Xiao T, Gao P, Li B, Sun W. Metabolic potentials of members of the class Acidobacteriia in metal-contaminated soils revealed by metagenomic analysis. Environ Microbiol 2021; 24:803-818. [PMID: 34081382 DOI: 10.1111/1462-2920.15612] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/18/2021] [Accepted: 05/23/2021] [Indexed: 01/09/2023]
Abstract
The relative abundance of Acidobacteriia correlated positively with the concentrations of arsenic (As), mercury (Hg), chromium (Cr), copper (Cu) and other metals, suggesting their adaptation of the metal-rich environments. Metagenomic binning reconstructed 29 high-quality metagenome-assembled genomes (MAGs) associated with Acidobacteriia, providing an opportunity to study their metabolic potentials. These MAGs contained genes to transform As, Hg and Cr through oxidation, reduction, efflux and demethylation, suggesting the potential of Acidobacteriia to transform such metal(loid)s. Additionally, genes associated with alleviation of acidic and metal stress were also detected in these MAGs. Acidobacteriia may have the capabilities to resist or transform metal(loid)s in acidic metal-contaminated sites. Moreover, these genes encoding metal transformation could be also identified in the Acidobacteriia-associated MAGs from five additional metal-contaminated sites across Southwest China, as well as Acidobacteriia-associated reference genomes from the NCBI database, suggesting that the capability of metal transformation may be widespread among Acidobacteriia members. This discovery provides an understanding of metabolic potentials of the Acidobacteriia in acidic metal-rich sites.
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Affiliation(s)
- Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, China
| | - Miaomiao Zhang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Zhaohui Yang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China
| | - Enzong Xiao
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Tangfu Xiao
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.,School of Environment, Henan Normal University, China.,Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, China
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11
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Kamusoko R, Jingura RM, Parawira W, Chikwambi Z. Purification and Amplification of DNA from Cellulolytic Bacteria: Application for Biogas Production from Crop Residues. Methods Mol Biol 2021; 2290:187-201. [PMID: 34009591 DOI: 10.1007/978-1-0716-1323-8_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Polymerase chain reaction (PCR) is a popular molecular tool for detection of bacteria. PCR allows millions of copies of a target segment of DNA to be produced. The DNA is extracted from overnight grown cultures of pure bacterial isolates using either the organo-solvent method or a commercial DNA extraction kit. The quality and purity of the DNA is determined by performing gel electrophoresis on 0.8% agarose gel. The DNA is amplified by performing PCR assay. Bands of approximately 1.5 kb in size are obtained from the amplified products of DNA. The PCR products run on 1.5% agarose gel are visualized with UV light and imaged by gel documentation system. This chapter outlines the protocol for isolation and amplification of DNA from cellulolytic bacteria. Cellulolytic bacteria are considered a potential source of cellulases for pretreatment of crop residues during biogas production. PCR is considered a very powerful, sensitive, specific, fast, and reliable tool in molecular detection and diagnostics.
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Affiliation(s)
- Reckson Kamusoko
- Department of Biotechnology, School of Agricultural Sciences and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe.
| | - Raphael M Jingura
- Department of Animal Production and Technology, School of Agricultural Sciences and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Wilson Parawira
- Faculty of Science, Bindura University of Science Education, Bindura, Zimbabwe
| | - Zedias Chikwambi
- Department of Biotechnology, School of Agricultural Sciences and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
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12
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Decomposition of roots of different diameters in response to different drought periods in a subtropical evergreen broad-leaf forest in Ailao Mountain. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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13
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Oberpaul M, Zumkeller CM, Culver T, Spohn M, Mihajlovic S, Leis B, Glaeser SP, Plarre R, McMahon DP, Hammann P, Schäberle TF, Glaeser J, Vilcinskas A. High-Throughput Cultivation for the Selective Isolation of Acidobacteria From Termite Nests. Front Microbiol 2020; 11:597628. [PMID: 33240253 PMCID: PMC7677567 DOI: 10.3389/fmicb.2020.597628] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/19/2020] [Indexed: 12/27/2022] Open
Abstract
Microbial communities in the immediate environment of socialized invertebrates can help to suppress pathogens, in part by synthesizing bioactive natural products. Here we characterized the core microbiomes of three termite species (genus Coptotermes) and their nest material to gain more insight into the diversity of termite-associated bacteria. Sampling a healthy termite colony over time implicated a consolidated and highly stable microbiome, pointing toward the fact that beneficial bacterial phyla play a major role in termite fitness. In contrast, there was a significant shift in the composition of the core microbiome in one nest during a fungal infection, affecting the abundance of well-characterized Streptomyces species (phylum Actinobacteria) as well as less-studied bacterial phyla such as Acidobacteria. High-throughput cultivation in microplates was implemented to isolate and identify these less-studied bacterial phylogenetic group. Amplicon sequencing confirmed that our method maintained the bacterial diversity of the environmental samples, enabling the isolation of novel Acidobacteriaceae and expanding the list of cultivated species to include two strains that may define new species within the genera Terracidiphilus and Acidobacterium.
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Affiliation(s)
- Markus Oberpaul
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Celine M. Zumkeller
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Tanja Culver
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Marius Spohn
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Sanja Mihajlovic
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Benedikt Leis
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Stefanie P. Glaeser
- Institute of Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Rudy Plarre
- Bundesanstalt für Materialforschung und -prüfung, Berlin, Germany
| | - Dino P. McMahon
- Bundesanstalt für Materialforschung und -prüfung, Berlin, Germany
- Institute of Biology, Free University of Berlin, Berlin, Germany
| | - Peter Hammann
- Sanofi-Aventis Deutschland GmbH, R&D Integrated Drug Discovery, Hoechst Industrial Park, Frankfurt am Main, Germany
| | - Till F. Schäberle
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Jens Glaeser
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Andreas Vilcinskas
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
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14
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Organic Carbon Storage and 14C Apparent Age of Upland and Riparian Soils in a Montane Subtropical Moist Forest of Southwestern China. FORESTS 2020. [DOI: 10.3390/f11060645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Upland and riparian soils usually differ in soil texture and moisture conditions, thus, likely varying in carbon storage and turnover time. However, few studies have differentiated their functions on the storage of soil organic carbon (SOC) in sub-tropical broad-leaved evergreen forests. In this study, we aim to uncover the SOC storage and 14C apparent age, in the upland and riparian soils of a primary evergreen broad-leaved montane subtropical moist forest in the Ailao Mountains of southwestern China. We sampled the upland and riparian soils along four soil profiles down to the parent material at regular intervals from two local representative watersheds, and determined SOC concentrations, δ13C values and 14C apparent ages. We found that SOC concentration decreased exponentially and 14C apparent age increased linearly with soil depth in the four soil profiles. Although, soil depth was deeper in the upland soil profiles than the riparian soil profiles, the weighted mean SOC concentration was significantly greater in the riparian soil (25.7 ± 3.9 g/kg) than the upland soil (19.7 ± 2.3 g/kg), but has an equal total SOC content per unit of ground area around 21 kg/m2 in the two different type soils. SOC δ13C values varied between −23.7 (±0.8)‰ and −33.2 (±0.2)‰ in the two upland soil profiles and between −25.5 (±0.4)‰ and −36.8 (±0.4)‰ along the two riparian soil profiles, with greater variation in the riparian soil profiles than the upland soil profiles. The slope of increase in SOC 14C apparent age along soil depth in the riparian soil profiles was greater than in the upland soil profiles. The oldest apparent age of SOC 14C was 23,260 (±230) years BP (before present, i.e., 1950) in the riparian soil profiles and 19,045 (±150) years BP in the upland soil profiles. Our data suggest that the decomposition of SOC is slower in the riparian soil than in the upland soil, and the increased SOC loss in the upland soil from deforestation may partially be compensated by the deposition of the eroded upland SOC in the riparian area, as an under-appreciated carbon sink.
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15
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Wang M, Wang C, Lan X, Abid AA, Xu X, Singla A, Sardans J, Llusià J, Peñuelas J, Wang W. Coupled steel slag and biochar amendment correlated with higher methanotrophic abundance and lower CH 4 emission in subtropical paddies. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2020; 42:483-497. [PMID: 31342217 DOI: 10.1007/s10653-019-00378-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/09/2019] [Indexed: 06/10/2023]
Abstract
Aerobic methanotrophs in paddies serve as methane (CH4) filters and thereby reduce CH4 emissions. Amending soil with waste products can mitigate CH4 emissions in crops, but little is known about the impacts of amendments with steel slag and biochar on the populations and activities of aerobic methanotrophs in rice cropland. We used real-time quantitative PCR detecting system and high-throughput sequencing to determine the effects of slag and biochar amendments on CH4 emission, abundance, and community structure of methanotrophs, and the relationships between soil properties and the abundance and community composition of methanotrophs during the rice growing season in both early and late paddies. Soil salinity and pH were significantly higher for an amendment with both slag and biochar than the control in both the early and late paddies, and pH was significantly higher for a slag amendment in the late paddy. Cumulative CH4 emission was lower for the slag and slag + biochar amendments than the control in early paddy by-34.1%. Methanotrophic abundance was three- and sixfold higher for the slag + biochar amendment than the control in the early and late paddies (p < 0.05), respectively. The abundance of different groups of methanotrophs varied among the treatments. The relative abundance of Methylosarcina was higher for the slag amendment than the control, and the relative abundance of Methylomonas was lower for biochar, and slag + biochar amendments than the control. The relative abundance of Methylocystis was higher for the slag and slag + biochar amendments than the control in the early paddy, and the relative abundance of Methylocystis was higher for the slag, biochar, and slag + biochar amendments in the late paddy. Univariate and multivariate analyses indicated that the higher abundance of methanotrophic bacteria for the slag and slag + biochar amendments was correlated with soil pH, salinity, soil organic carbon, and C/N ratio, and the relative abundances of Methylocystis, Methylomonas, and Methylosarcina were associated with the effective mitigation of CH4 emission in the paddies. A discriminant general analysis indicated that the total population of methanotrophs was larger for the slag + biochar amendment than the control, and that this effect was only weakly correlated with changes in the soil properties, demonstrating that this effect on the size and species composition of methanotrophic soil populations was mostly associated with a direct effect of the slag + biochar amendment.
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Affiliation(s)
- Miaoying Wang
- College of Life Science, Fujian Normal University, Fuzhou, 350108, China
| | - Chun Wang
- Key Laboratory of Humid Sub-tropical Eco-geographical Process of Ministry of Education, Fujian Normal University, Fuzhou, 350007, China
| | - Xingfu Lan
- College of Life Science, Fujian Normal University, Fuzhou, 350108, China
| | - Abbas Ali Abid
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xuping Xu
- College of Life Science, Fujian Normal University, Fuzhou, 350108, China.
| | - Ankit Singla
- Regional Centre of Organic Farming, Ministry of Agriculture and Farmers Welfare, Bhubaneswar, Odisha, 751-021, India
| | - Jordi Sardans
- Global Ecology Unit, CREAF-CSIC-UAB, CSIC, 08193, Bellaterra, Catalonia, Spain.
- CREAF, 08193, Cerdanyola del Vallès, Catalonia, Spain.
| | - Joan Llusià
- Global Ecology Unit, CREAF-CSIC-UAB, CSIC, 08193, Bellaterra, Catalonia, Spain
- CREAF, 08193, Cerdanyola del Vallès, Catalonia, Spain
| | - Josep Peñuelas
- Global Ecology Unit, CREAF-CSIC-UAB, CSIC, 08193, Bellaterra, Catalonia, Spain
- CREAF, 08193, Cerdanyola del Vallès, Catalonia, Spain
| | - Weiqi Wang
- Key Laboratory of Humid Sub-tropical Eco-geographical Process of Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
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16
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The Influence of Land Use Patterns on Soil Bacterial Community Structure in the Karst Graben Basin of Yunnan Province, China. FORESTS 2019. [DOI: 10.3390/f11010051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Land use patterns can change the structure of soil bacterial communities. However, there are few studies on the effects of land use patterns coupled with soil depth on soil bacterial communities in the karst graben basin of Yunnan province, China. Consequently, to reveal the structure of the soil bacterial community at different soil depths across land use changes in the graben basins of the Yunnan plateau, the relationship between soil bacterial communities and soil physicochemical properties was investigated for a given area containing woodland, shrubland, and grassland in Yunnan province by using next-generation sequencing technologies coupled with soil physicochemical analysis. Our results indicated that the total phosphorus (TP), available potassium (AK), exchangeable magnesium (E-Mg), and electrical conductivity (EC) in the grassland were significantly higher than those in the woodland and shrubland, yet the total nitrogen (TN) and soil organic carbon (SOC) in the woodland were higher than those in the shrubland and grassland. Proteobacteria, Verrucomicrobia, and Acidobacteria were the dominant bacteria, and their relative abundances were different in the three land use types. SOC, TN, and AK were the most important factors affecting soil bacterial communities. Land use exerts strong effects on the soil bacterial community structure in the soil’s surface layer, and the effects of land use attenuation decrease with soil depth. The nutrient content of the soil surface layer was higher than that of the deep layer, which was more suitable for the survival and reproduction of bacteria in the surface layer.
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17
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Yuan C, Zhu G, Yang S, Xu G, Li Y, Gong H, Wu C. Soil warming increases soil temperature sensitivity in subtropical Forests of SW China. PeerJ 2019; 7:e7721. [PMID: 31579603 PMCID: PMC6765358 DOI: 10.7717/peerj.7721] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/22/2019] [Indexed: 11/20/2022] Open
Abstract
Background Soil respiration (RS) plays an important role in the concentration of atmospheric CO2 and thus in global climate patterns. Due to the feedback between RS and climate, it is important to investigate RS responses to climate warming. Methods A soil warming experiment was conducted to explore RS responses and temperature sensitivity (Q10) to climate warming in subtropical forests in Southwestern China, and infrared radiators were used to simulate climate warming. Results Warming treatment increased the soil temperature and RS value by 1.4 °C and 7.3%, respectively, and decreased the soil water level by 4.2% (%/%). Both one- and two-factor regressions showed that warming increased the Q10 values by 89.1% and 67.4%, respectively. The effects of water on Q10show a parabolic relationship to the soil water sensitivity coefficient. Both RS and Q10 show no acclimation to climate warming, suggesting that global warming will accelerate soil carbon release.
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Affiliation(s)
- Chaoxiang Yuan
- School of Geography and Ecotourism, Southwest Forestry University, Kunming, China
| | - Guiqing Zhu
- School of Geography and Ecotourism, Southwest Forestry University, Kunming, China
| | - Shuangna Yang
- School of Geography and Ecotourism, Southwest Forestry University, Kunming, China
| | - Gang Xu
- School of Geography and Ecotourism, Southwest Forestry University, Kunming, China
| | - Yingyun Li
- School of Geography and Ecotourism, Southwest Forestry University, Kunming, China
| | - Hede Gong
- School of Geography and Ecotourism, Southwest Forestry University, Kunming, China
| | - Chuansheng Wu
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, China
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18
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de Chaves MG, Silva GGZ, Rossetto R, Edwards RA, Tsai SM, Navarrete AA. Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers. Front Microbiol 2019; 10:1680. [PMID: 31417506 PMCID: PMC6682628 DOI: 10.3389/fmicb.2019.01680] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/08/2019] [Indexed: 11/21/2022] Open
Abstract
Acidobacteria is a predominant bacterial phylum in tropical agricultural soils, including sugarcane cultivated soils. The increased need for fertilizers due to the expansion of sugarcane production is a threat to the ability of the soil to maintain its potential for self-regulation in the long term, in witch carbon degradation has essential role. In this study, a culture-independent approach based on high-throughput DNA sequencing and microarray technology was used to perform taxonomic and functional profiling of the Acidobacteria community in a tropical soil under sugarcane (Saccharum spp.) that was supplemented with nitrogen (N) combined with vinasse. These analyses were conducted to identify the subgroup-level responses to chemical changes and the carbon (C) degradation potential of the different Acidobacteria subgroups. Eighteen Acidobacteria subgroups from a total of 26 phylogenetically distinct subgroups were detected based on high-throughput DNA sequencing, and 16 gene families associated with C degradation were quantified using Acidobacteria-derived DNA microarray probes. The subgroups Gp13 and Gp18 presented the most positive correlations with the gene families associated with C degradation, especially those involved in hemicellulose degradation. However, both subgroups presented low abundance in the treatment containing vinasse. In turn, the Gp4 subgroup was the most abundant in the treatment that received vinasse, but did not present positive correlations with the gene families for C degradation analyzed in this study. The metabolic potential for C degradation of the different Acidobacteria subgroups in sugarcane soil amended with N and vinasse can be driven in part through the increase in soil nutrient availability, especially calcium (Ca), magnesium (Mg), potassium (K), aluminum (Al), boron (B) and zinc (Zn). This soil management practice reduces the abundance of Acidobacteria subgroups, including those potentially involved with C degradation in this agricultural soil.
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Affiliation(s)
- Miriam Gonçalves de Chaves
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Raffaella Rossetto
- São Paulo's Agency for Agribusiness Technology APTA-SAA, Piracicaba, Brazil
| | - Robert Alan Edwards
- Computational Science Research Center, San Diego State University, San Diego, CA, United States
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Acacio Aparecido Navarrete
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil.,Department of Environmental Sciences, Federal University of São Carlos, Sorocaba, Brazil
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19
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Wu Q, Lu C, Ni M, Wang H, Liu W, Chen J. Streptomyces lydicus A01 affects soil microbial diversity, improving growth and resilience in tomato. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:182-196. [PMID: 30255551 DOI: 10.1111/jipb.12724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/18/2018] [Indexed: 05/27/2023]
Abstract
The actinomycete Streptomyces lydicus A01 promotes tomato seedling growth; however, the underlying mechanism is unclear. In this study, we investigated whether changes in soil microbial diversity, following Streptomyces lydicus A01 treatment, were responsible for the increased tomato seedling growth. Eukaryotic 18S ribosomal DNA (rDNA) sequencing showed that S. lydicus A01-treated and untreated soil shared 193 operational taxonomic units (OTUs), whereas bacterial 16S rDNA sequencing identified 1,219 shared OTUs between the treated and untreated soil. Of the 42 dominant eukaryotic OTUs, eight were significantly increased and six were significantly decreased after A01 treatment. Of the 25 dominant bacterial OTUs, 12 were significantly increased and eight were significantly decreased after A01 treatment. Most of the eukaryotes and bacteria that increased in abundance exhibited growth promoting characteristics, which were mainly predicted to be associated with mineralization of nitrogen and phosphorus, phosphate solubilization, nutrient accumulation, and secretion of auxin, whereas some were related to plant protection, such as the degradation of toxic and hazardous substances. Soil composition tests showed that S. lydicus A01 treatment enhanced the utilization of nitrogen, phosphorus, and potassium in tomato seedlings. Thus, microbial fertilizers based on S. lydicus A01 may improve plant growth, without the detriment effects of chemical fertilizers.
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Affiliation(s)
- Qiong Wu
- The Key laboratory of Urban (South) Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Laboratory of Biological Microbiology, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Caige Lu
- Laboratory of Biological Microbiology, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Mi Ni
- Laboratory of Biological Microbiology, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Hongli Wang
- Laboratory of Biological Microbiology, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Weicheng Liu
- Laboratory of Biological Microbiology, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jie Chen
- The Key laboratory of Urban (South) Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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20
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Mumtaz S, Streten C, Parry DL, McGuinness KA, Lu P, Gibb KS. Soil uranium concentration at Ranger Uranium Mine Land Application Areas drives changes in the bacterial community. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2018; 189:14-23. [PMID: 29549875 DOI: 10.1016/j.jenvrad.2018.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/08/2018] [Accepted: 03/08/2018] [Indexed: 06/08/2023]
Abstract
Soil microorganisms may respond to metal stress by a shift in the microbial community from metal sensitive to metal resistant microorganisms. We assessed the bacterial community from low (2-20 mg kg-1), medium (200-400 mg kg-1), high (500-900 mg kg-1) and very high (>900 mg kg-1) uranium soils at Ranger Uranium Mine in northern Australia through pyrosequencing. Proteobacteria (28.85%) was the most abundant phylum at these sites, followed by Actinobacteria (9.31%), Acidobacteria (7.33%), Verrucomicrobia (2.11%), Firmicutes (2.02%), Chloroflexi (1.11%), Cyanobacteria (0.93%), Planctomycetes (0.82%), Bacteroidetes (0.46%) and Candidate_division_WS3 (Latescibacteria) (0.21%). However, 46.79% of bacteria were unclassified. Bacteria at low U soils differed from soils with elevated uranium. Bacterial OTUs closely related to Kitasatospora spp., Sphingobacteria spp. and Rhodobium spp. were only present at higher uranium concentrations and the bacterial community also changed with seasonal and temporal changes in soil uranium and physicochemical variables. This study using next generation sequencing in association with environmental variables at a uranium mine has laid a foundation for further studies of soil-microbe-metal interactions which may be useful for developing sustainable management and rehabilitation strategies. Furthermore, bacterial species associated with higher uranium may serve as useful indicators of uranium contamination in the wet-dry tropics.
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Affiliation(s)
- Saqib Mumtaz
- Charles Darwin University, Darwin, NT, Australia.
| | | | - David L Parry
- Charles Darwin University, Darwin, NT, Australia; Australian Institute of Marine Science, Darwin, NT, Australia
| | | | - Ping Lu
- Charles Darwin University, Darwin, NT, Australia; Energy Resources of Australia, Darwin, NT, Australia
| | - Karen S Gibb
- Charles Darwin University, Darwin, NT, Australia
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21
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Fei X, Song Q, Zhang Y, Liu Y, Sha L, Yu G, Zhang L, Duan C, Deng Y, Wu C, Lu Z, Luo K, Chen A, Xu K, Liu W, Huang H, Jin Y, Zhou R, Li J, Lin Y, Zhou L, Fu Y, Bai X, Tang X, Gao J, Zhou W, Grace J. Carbon exchanges and their responses to temperature and precipitation in forest ecosystems in Yunnan, Southwest China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 616-617:824-840. [PMID: 29100686 DOI: 10.1016/j.scitotenv.2017.10.239] [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: 08/25/2017] [Revised: 10/21/2017] [Accepted: 10/22/2017] [Indexed: 06/07/2023]
Abstract
Forest ecosystems play an increasingly important role in the global carbon cycle. However, knowledge on carbon exchanges, their spatio-temporal patterns, and the extent of the key controls that affect carbon fluxes is lacking. In this study, we employed 29-site-years of eddy covariance data to observe the state, spatio-temporal variations and climate sensitivity of carbon fluxes (gross primary productivity (GPP), ecosystem respiration (Reco), and net ecosystem carbon exchange (NEE)) in four representative forest ecosystems in Yunnan. We found that 1) all four forest ecosystems were carbon sinks (the average NEE was -3.40tCha-1yr-1); 2) contrasting seasonality of the NEE among the ecosystems with a carbon sink mainly during the wet season in the Yuanjiang savanna ecosystem (YJ) but during the dry season in the Xishuangbanna tropical rainforest ecosystem (XSBN), besides an equivalent NEE uptake was observed during the wet/dry season in the Ailaoshan subtropical evergreen broad-leaved forest ecosystem (ALS) and Lijiang subalpine coniferous forest ecosystem (LJ); 3) as the GPP increased, the net ecosystem production (NEP) first increased and then decreased when the GPP>17.5tCha-1yr-1; 4) the precipitation determines the carbon sinks in the savanna ecosystem (e.g., YJ), while temperature did so in the tropical forest ecosystem (e.g., XSBN); 5) overall, under the circumstances of warming and decreased precipitation, the carbon sink might decrease in the YJ but maybe increase in the ALS and LJ, while future strength of the sink in the XSBN is somewhat uncertain. However, based on the redundancy analysis, the temperature and precipitation combined together explained 39.7%, 32.2%, 25.3%, and 29.6% of the variations in the NEE in the YJ, XSBN, ALS and LJ, respectively, which indicates that considerable changes in the NEE could not be explained by variations in the temperature and precipitation. Therefore, the effects of other factors (e.g., CO2 concentration, N/P deposition, aerosol and other variables) on the NEE still require extensive research and need to be considered seriously in carbon-cycle-models.
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Affiliation(s)
- Xuehai Fei
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Global Change Ecology Group, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinghai Song
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Global Change Ecology Group, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China.
| | - Yiping Zhang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Global Change Ecology Group, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China.
| | - Yuntong Liu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Global Change Ecology Group, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China
| | - Liqing Sha
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Global Change Ecology Group, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China
| | - Guirui Yu
- Synthesis Research Center of Chinese Ecosystem Research Network, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Leiming Zhang
- Synthesis Research Center of Chinese Ecosystem Research Network, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Changqun Duan
- Institute of Environmental Sciences and Ecological Restoration, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China
| | - Yun Deng
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Xishuangbanna Station for Tropical Rainforest Ecosystem Studies, Menglun, Xishuangbanna, Yunnan 666303, China
| | - Chuansheng Wu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Ailaoshan Station for Subtropical Forest Ecosystem Studies, Jingdong, Yunnan 676209, China
| | - Zhiyun Lu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Ailaoshan Station for Subtropical Forest Ecosystem Studies, Jingdong, Yunnan 676209, China
| | - Kang Luo
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China; Ailaoshan Station for Subtropical Forest Ecosystem Studies, Jingdong, Yunnan 676209, China
| | - Aiguo Chen
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Yuanjiang Savanna Ecosystem Research Station, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yuanjiang, Yunnan 653300, China
| | - Kun Xu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Lijiang Forest Ecosystem Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, 132# Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
| | - Weiwei Liu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Lijiang Forest Ecosystem Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, 132# Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
| | - Hua Huang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Lijiang Forest Ecosystem Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, 132# Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
| | - Yanqiang Jin
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Global Change Ecology Group, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruiwu Zhou
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Global Change Ecology Group, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Li
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Global Change Ecology Group, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Youxing Lin
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Global Change Ecology Group, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liguo Zhou
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Global Change Ecology Group, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yane Fu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolong Bai
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianhui Tang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Global Change Ecology Group, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinbo Gao
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Global Change Ecology Group, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjun Zhou
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Global Change Ecology Group, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China
| | - John Grace
- School of GeoSciences, The University of Edinburgh, Edinburgh EH9 3FF, UK
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Damsté JSS, Rijpstra WIC, Dedysh SN, Foesel BU, Villanueva L. Pheno- and Genotyping of Hopanoid Production in Acidobacteria. Front Microbiol 2017; 8:968. [PMID: 28642737 PMCID: PMC5462960 DOI: 10.3389/fmicb.2017.00968] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/15/2017] [Indexed: 11/28/2022] Open
Abstract
Hopanoids are pentacyclic triterpenoid lipids synthesized by different bacterial groups. Methylated hopanoids were believed to be exclusively synthesized by cyanobacteria and aerobic methanotrophs until the genes encoding for the methylation at the C-2 and C-3 position (hpnP and hpnR) were found to be widespread in the bacterial domain, invalidating their use as specific biomarkers. These genes have been detected in the genome of the Acidobacterium "Ca. Koribacter versatilis," but our knowledge of the synthesis of hopanoids and the presence of genes of their biosynthetic pathway in other member of the Acidobacteria is limited. We analyzed 38 different strains of seven Acidobacteria subdivisions (SDs 1, 3, 4, 6, 8, 10, and 23) for the presence of C30 hopenes and C30+ bacteriohopane polyols (BHPs) using the Rohmer reaction. BHPs and/or C30 hopenes were detected in all strains of SD1 and SD3 but not in SD4 (excepting Chloracidobacterium thermophilum), 6, 8, 10, and 23. This is in good agreement with the presence of genes required for hopanoid biosynthesis in the 31 available whole genomes of cultivated Acidobacteria. All genomes encode the enzymes involved in the non-mevalonate pathway ultimately leading to farnesyl diphosphate but only SD1 and 3 Acidobacteria and C. thermophilum encode all three enzymes required for the synthesis of squalene, its cyclization (shc), and addition and modification of the extended side chain (hpnG, hpnH, hpnI, hpnJ, hpnO). In almost all strains, only tetrafunctionalized BHPs were detected; three strains contained variable relative abundances (up to 45%) of pentafunctionalized BHPs. Only "Ca. K. versatilis" contained methylated hopanoids (i.e., 2,3-dimethyl bishomohopanol), although in low (<10%) amounts. These genes are not present in any other Acidobacterium, consistent with the absence of methylated BHPs in the other examined strains. These data are in agreement with the scattered occurrence of methylated BHPs in other bacterial phyla such as the Alpha-, Beta-, and Gammaproteobacteria and the Cyanobacteria, limiting their biomarker potential. Metagenomes of Acidobacteria were also examined for the presence of genes required for hopanoid biosynthesis. The complete pathway for BHP biosynthesis was evident in SD2 Acidobacteria and a group phylogenetically related to SD1 and SD3, in line with the limited occurrence of BHPs in acidobacterial cultures.
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Affiliation(s)
- Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands
- Department of Earth Sciences, Geochemistry, Faculty of Geosciences, Utrecht UniversityUtrecht, Netherlands
| | - W. Irene C. Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands
| | - Svetlana N. Dedysh
- S. N. Winogradsky Institute of Microbiology, Research Center of Biotechnology of Russian Academy of SciencesMoscow, Russia
| | - Bärbel U. Foesel
- Department of Microbial Ecology and Diversity Research, German Collection of Microorganisms and Cell Cultures (LG)Braunschweig, Germany
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands
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23
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Nizami SM, Yiping Z, Zheng Z, Zhiyun L, Guoping Y, Liqing S. Evaluation of forest structure, biomass and carbon sequestration in subtropical pristine forests of SW China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:8137-8146. [PMID: 28144865 DOI: 10.1007/s11356-017-8506-7] [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: 03/05/2016] [Accepted: 01/24/2017] [Indexed: 06/06/2023]
Abstract
Very old natural forests comprising the species of Fagaceae (Lithocarpus xylocarpus, Castanopsis wattii, Lithocarpus hancei) have been prevailing since years in the Ailaoshan Mountain Nature Reserve (AMNR) SW China. Within these forest trees, density is quite variable. We studied the forest structure, stand dynamics and carbon density at two different sites to know the main factors which drives carbon sequestration process in old forests by considering the following questions: How much is the carbon density in these forest trees of different DBH (diameter at breast height)? How much carbon potential possessed by dominant species of these forests? How vegetation carbon is distributed in these forests? Which species shows high carbon sequestration? What are the physiochemical properties of soil in these forests? Five-year (2005-2010) tree growth data from permanently established plots in the AMNR was analysed for species composition, density, stem diameter (DBH), height and carbon (C) density both in aboveground and belowground vegetation biomass. Our study indicated that among two comparative sites, overall 54 species of 16 different families were present. The stem density, height, C density and soil properties varied significantly with time among the sites showing uneven distribution across the forests. Among the dominant species, L. xylocarpus represents 30% of the total carbon on site 1 while C. wattii represents 50% of the total carbon on site 2. The average C density ranged from 176.35 to 243.97 t C ha-1. The study emphasized that there is generous degree to expand the carbon stocking in this AMNR through scientific management gearing towards conservation of old trees and planting of potentially high carbon sequestering species on good site quality areas.
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Affiliation(s)
- Syed Moazzam Nizami
- Key Laboratory for Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666300, China.
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- IMARC Karakoram International University, Gilgit, Gilgit-Baltistan, 15100, Pakistan.
| | - Zhang Yiping
- Key Laboratory for Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666300, China
- Ailaoshan Station for Subtropical Forest Ecosystem Research, Yunnan, 676209, China
| | - Zheng Zheng
- Key Laboratory for Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666300, China
- Ailaoshan Station for Subtropical Forest Ecosystem Research, Yunnan, 676209, China
| | - Lu Zhiyun
- Ailaoshan Station for Subtropical Forest Ecosystem Research, Yunnan, 676209, China
| | - Yang Guoping
- Ailaoshan Station for Subtropical Forest Ecosystem Research, Yunnan, 676209, China
| | - Sha Liqing
- Key Laboratory for Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666300, China
- Ailaoshan Station for Subtropical Forest Ecosystem Research, Yunnan, 676209, China
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24
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Water use efficiency in a primary subtropical evergreen forest in Southwest China. Sci Rep 2017; 7:43031. [PMID: 28216656 PMCID: PMC5316949 DOI: 10.1038/srep43031] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/18/2017] [Indexed: 11/08/2022] Open
Abstract
We calculated water use efficiency (WUE) using measures of gross primary production (GPP) and evapotranspiration (ET) from five years of continuous eddy covariance measurements (2009–2013) obtained over a primary subtropical evergreen broadleaved forest in southwestern China. Annual mean WUE exhibited a decreasing trend from 2009 to 2013, varying from ~2.28 to 2.68 g C kg H2O−1. The multiyear average WUE was 2.48 ± 0.17 (mean ± standard deviation) g C kg H2O−1. WUE increased greatly in the driest year (2009), due to a larger decline in ET than in GPP. At the diurnal scale, WUE in the wet season reached 5.1 g C kg H2O−1 in the early morning and 4.6 g C kg H2O−1 in the evening. WUE in the dry season reached 3.1 g C kg H2O−1 in the early morning and 2.7 g C kg H2O−1 in the evening. During the leaf emergence stage, the variation of WUE could be suitably explained by water-related variables (relative humidity (RH), soil water content at 100 cm (SWC_100)), solar radiation and the green index (Sgreen). These results revealed large variation in WUE at different time scales, highlighting the importance of individual site characteristics.
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25
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Effect of 40 and 80 Years of Conifer Regrowth on Soil Microbial Activities and Community Structure in Subtropical Low Mountain Forests. FORESTS 2016. [DOI: 10.3390/f7100244] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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Myers MR, King GM. Isolation and characterization of Acidobacterium ailaaui sp. nov., a novel member of Acidobacteria subdivision 1, from a geothermally heated Hawaiian microbial mat. Int J Syst Evol Microbiol 2016; 66:5328-5335. [PMID: 27692038 DOI: 10.1099/ijsem.0.001516] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A novel member of Acidobacteria was isolated from a microbial mat growing on a geothermally heated dead tree trunk in Hawai'i Volcanoes National Park (HI, USA). The rod-shaped, Gram-negative capsulated cells of strain PMMR2T were non-motile and catalase and oxidase negative. Growth occurred aerobically from 15 to 55 °C (optimum, 40 °C) and at pH values from 4.5 to 7.0 (optimum, 6.5). A limited range of sugars and organic acids supported growth. However, results of a genomic analysis suggested that various polysaccharides might be hydrolysed as carbon sources, and evidence for pectin degradation was observed in liquid cultures. A genomic analysis also revealed genes for a Group 1f uptake hydrogenase; assays with liquid cultures confirmed hydrogen consumption, including uptake at sub-atmospheric concentrations. Nitrate was not dissimilated to nitrite. Major membrane fatty acids included iso-C15 : 0 and iso-C17 : 0. The G+C content was 57.2mol%. A comparative genome analysis revealed an average nucleotide identity of 72.2 % between PMMR2T and its nearest cultured phylogenetic neighbour, Acidobacterium capsulatum ATCC 51196T (=JCM 7670T); analysis of the 16S rRNA gene revealed a 96.8 % sequence identity with Acidobacterium capsulatum ATCC 51196T. These results and other phenotypic differences indicated that strain PMMR2T represents a novel species in the genus Acidobacterium, for which the name Acidobacterium ailaaui sp. nov. is proposed. The type strain, PMMR2T (=DSM 27394T=LMG 28340T), is the second formal addition to the genus Acidobacterium.
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Affiliation(s)
- Marisa R Myers
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - G M King
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
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27
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Kielak AM, Barreto CC, Kowalchuk GA, van Veen JA, Kuramae EE. The Ecology of Acidobacteria: Moving beyond Genes and Genomes. Front Microbiol 2016; 7:744. [PMID: 27303369 PMCID: PMC4885859 DOI: 10.3389/fmicb.2016.00744] [Citation(s) in RCA: 454] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 05/03/2016] [Indexed: 12/01/2022] Open
Abstract
The phylum Acidobacteria is one of the most widespread and abundant on the planet, yet remarkably our knowledge of the role of these diverse organisms in the functioning of terrestrial ecosystems remains surprisingly rudimentary. This blatant knowledge gap stems to a large degree from the difficulties associated with the cultivation of these bacteria by classical means. Given the phylogenetic breadth of the Acidobacteria, which is similar to the metabolically diverse Proteobacteria, it is clear that detailed and functional descriptions of acidobacterial assemblages are necessary. Fortunately, recent advances are providing a glimpse into the ecology of members of the phylum Acidobacteria. These include novel cultivation and enrichment strategies, genomic characterization and analyses of metagenomic DNA from environmental samples. Here, we couple the data from these complementary approaches for a better understanding of their role in the environment, thereby providing some initial insights into the ecology of this important phylum. All cultured acidobacterial type species are heterotrophic, and members of subdivisions 1, 3, and 4 appear to be more versatile in carbohydrate utilization. Genomic and metagenomic data predict a number of ecologically relevant capabilities for some acidobacteria, including the ability to: use of nitrite as N source, respond to soil macro-, micro nutrients and soil acidity, express multiple active transporters, degrade gellan gum and produce exopolysaccharide (EPS). Although these predicted properties allude to a competitive life style in soil, only very few of these prediction shave been confirmed via physiological studies. The increased availability of genomic and physiological information, coupled to distribution data in field surveys and experiments, should direct future progress in unraveling the ecology of this important but still enigmatic phylum.
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Affiliation(s)
- Anna M Kielak
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
| | - Cristine C Barreto
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília Brasília, Brazil
| | - George A Kowalchuk
- Ecology and Biodiversity Group, University of Utrecht Utrecht, Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
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28
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Zeng Q, Dong Y, An S. Bacterial Community Responses to Soils along a Latitudinal and Vegetation Gradient on the Loess Plateau, China. PLoS One 2016; 11:e0152894. [PMID: 27045518 PMCID: PMC4821562 DOI: 10.1371/journal.pone.0152894] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/21/2016] [Indexed: 11/19/2022] Open
Abstract
Soil bacterial communities play an important role in nutrient recycling and storage in terrestrial ecosystems. Loess soils are one of the most important soil resources for maintaining the stability of vegetation ecosystems and are mainly distributed in northwest China. Estimating the distributions and affecting factors of soil bacterial communities associated with various types of vegetation will inform our understanding of the effect of vegetation restoration and climate change on these processes. In this study, we collected soil samples from 15 sites from north to south on the Loess Plateau of China that represent different ecosystem types and analyzed the distributions of soil bacterial communities by high-throughput 454 pyrosequencing. The results showed that the 142444 sequences were grouped into 36816 operational taxonomic units (OTUs) based on 97% similarity. The results of the analysis showed that the dominant taxonomic phyla observed in all samples were Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria and Planctomycetes. Actinobacteria and Proteobacteria were the two most abundant groups in all samples. The relative abundance of Actinobacteria increased from 14.73% to 40.22% as the ecosystem changed from forest to sandy, while the relative abundance of Proteobacteria decreased from 35.35% to 21.40%. Actinobacteria and Proteobacteria had significant correlations with mean annual precipitation (MAP), pH, and soil moisture and nutrients. MAP was significantly correlated with soil chemical and physical properties. The relative abundance of Actinobacteria, Proteobacteria and Planctomycetes correlated significantly with MAP, suggesting that MAP was a key factor that affected the soil bacterial community composition. However, along with the MAP gradient, Chloroflexi, Bacteroidetes and Cyanobacteria had narrow ranges that did not significantly vary with the soil and environmental factors. Overall, we conclude that the edaphic properties and/or vegetation types are driving bacterial community composition. MAP was a key factor that affects the composition of the soil bacteria on the Loess Plateau of China.
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Affiliation(s)
- Quanchao Zeng
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Yanghong Dong
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Shaoshan An
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, P.R. China
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Northwest A&F University, Yangling, Shaanxi, P.R. China
- * E-mail:
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Dynamic diversification of bacterial functional groups in the Baiyunbian liquor stacking fermentation process. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-016-1211-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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30
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Heterotrophic respiration does not acclimate to continuous warming in a subtropical forest. Sci Rep 2016; 6:21561. [PMID: 26900028 PMCID: PMC4761939 DOI: 10.1038/srep21561] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 01/26/2016] [Indexed: 11/08/2022] Open
Abstract
As heterotrophic respiration (RH) has great potential to increase atmospheric CO2 concentrations, it is important to understand warming effects on RH for a better prediction of carbon–climate feedbacks. However, it remains unclear how RH responds to warming in subtropical forests. Here, we carried out trenching alone and trenching with warming treatments to test the climate warming effect on RH in a subtropical forest in southwestern China. During the measurement period, warming increased annual soil temperature by 2.1 °C, and increased annual mean RH by 22.9%. Warming effect on soil temperature (WET) showed very similar pattern with warming effect on RH (WERH), decreasing yearly. Regression analyses suggest that WERH was controlled by WET and also regulated by the soil water content. These results showed that the decrease of WERH was not caused by acclimation to the warmer temperature, but was instead due to decrease of WET. We therefore suggest that global warming will accelerate soil carbon efflux to the atmosphere, regulated by the change in soil water content in subtropical forests.
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Mumtaz S, Streten C, Parry DL, McGuinness KA, Lu P, Gibb KS. Land application of mine water causes minimal uranium loss offsite in the wet-dry tropics: Ranger Uranium Mine, Northern Territory, Australia. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2015; 149:121-128. [PMID: 26233650 DOI: 10.1016/j.jenvrad.2015.07.014] [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: 02/06/2015] [Revised: 07/15/2015] [Accepted: 07/15/2015] [Indexed: 06/04/2023]
Abstract
Ranger Uranium Mine (RUM) is situated in the wet-dry tropics of Northern Australia. Land application (irrigation) of stockpile (ore and waste) runoff water to natural woodland on the mine lease is a key part of water management at the mine. Consequently, the soil in these Land Application Areas (LAAs) presents a range of uranium (U) and other metals concentrations. Knowledge of seasonal and temporal changes in soil U and physicochemical parameters at RUM LAAs is important to develop suitable management and rehabilitation strategies. Therefore, soil samples were collected from low, medium, high and very high U sites at RUM LAAs for two consecutive years and the effect of time and season on soil physicochemical parameters particularly U and other major solutes applied in irrigation water was measured. Concentrations of some of the solutes applied in the irrigation water such as sulphur (S), iron (Fe) and calcium (Ca) showed significant seasonal and temporal changes. Soil S, Fe and Ca concentration decreased from year 1 to year 2 and from dry to wet seasons during both years. Soil U followed the same pattern except that we recorded an increase in soil U concentrations at most of the RUM LAAs after year 2 wet season compared to year 2 dry season. Thus, these sites did not show a considerable decrease in soil U concentration from year 1 to year 2. Sites which contained elevated U after wet season 2 also had higher moisture content which suggests that pooling of U containing rainwater at these sites may be responsible for elevated U. Thus, U may be redistributed within RUM LAAs due to surface water movement. The study also suggested that a decrease in U concentrations in LAA soils at very high U (>900 mg kg(-1)) sites is most likely due to transport of particulate matter bound U by surface runoff and U may not be lost from the surface soil due to vertical movement through the soil profile. Uranium attached to particulate matter may reduce its potential for environmental impact. These findings suggest that U is effectively adsorbed by the soils and thus land application may serve as a useful tool for U management in the wet-dry tropics of northern Australia.
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Affiliation(s)
- Saqib Mumtaz
- Charles Darwin University, Darwin, NT, Australia.
| | | | - David L Parry
- Australian Institute of Marine Science, Darwin, NT, Australia.
| | | | - Ping Lu
- Energy Resources of Australia, Darwin, NT, Australia.
| | - Karen S Gibb
- Charles Darwin University, Darwin, NT, Australia.
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32
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Kim JS, Lee KC, Kim DS, Ko SH, Jung MY, Rhee SK, Lee JS. Pyrosequencing analysis of a bacterial community associated with lava-formed soil from the Gotjawal forest in Jeju, Korea. Microbiologyopen 2015; 4:301-312. [PMID: 25604185 PMCID: PMC4398510 DOI: 10.1002/mbo3.238] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 12/04/2014] [Accepted: 12/12/2014] [Indexed: 02/01/2023] Open
Abstract
In this study, we analyzed the bacterial diversity in soils collected from Gyorae Gotjawal forest, where globally unique topography, geology, and ecological features support a forest grown on basalt flows from 110,000 to 120,000 years ago and 40,000 to 50,000 years ago. The soils at the site are fertile, with rocky areas, and are home to endangered species of plants and animals. Rainwater penetrates to the groundwater aquifer, which is composed of 34% organic matter containing rare types of soil and no soil profile. We determined the bacterial community composition using 116,475 reads from a 454-pyrosequencing analysis. This dataset included 12,621 operational taxonomic units at 3% dissimilarity, distributed among the following groups: Proteobacteria (56.2%) with 45.7% of α-Proteobacteria, Actinobacteria (25%), Acidobacteria (10.9%), Chloroflexi (2.4%), and Bacteroidetes (0.9%). In addition, 16S rRNA gene sequences were amplified using polymerase chain reaction and domain-specific primers to construct a clone library based on 142 bacterial clones. These clones were affiliated with the following groups: Proteobacteria (56%) with 51% of α-Proteobacteria, Acidobacteria (7.8%), Actinobacteria (17.6%), Chloroflexi (2.1%), Bacilli (1.4%), Cyanobacteria (2.8%), and Planctomycetes (1.4%). Within the phylum Proteobacteria, 56 of 80 clones were tentatively identified as 12 unclassified genera. Several new genera and a new family were discovered within the Actinobacteria clones. Results from 454-pyrosequencing revealed that 57% and 34% of the sequences belonged to undescribed genera and families, respectively. The characteristics of Gotjawal soil, which are determined by lava morphology, vegetation, and groundwater penetration, might be reflected in the bacterial community composition.
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Affiliation(s)
- Jong-Shik Kim
- Gyeongbuk Institute for Marine Bioindustry, Uljin, 767-813, Korea
| | - Keun Chul Lee
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
| | - Dae-Shin Kim
- Research Institute for Hallasan, Jeju Special Self-Governing Province, 690-816, Korea
| | - Suk-Hyung Ko
- Research Institute for Hallasan, Jeju Special Self-Governing Province, 690-816, Korea
| | - Man-Young Jung
- Department of Microbiology, Chungbuk National University, Cheongju, 361-763, Korea
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, 361-763, Korea
| | - Jung-Sook Lee
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
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33
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Li Y, Yang G, Neher DA, Xu CY, Wu J. Status of soil nematode communities during natural regeneration of a subtropical forest in southwestern China. NEMATOLOGY 2015. [DOI: 10.1163/15685411-00002853] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Forest recovery has been extensively evaluated using plant communities but fewer studies have been conducted on soil fauna. This study reports the status of soil nematode communities during natural re-establishment after deforestation in a subtropical forest in southwestern China. Soil nematode communities of two secondary succession stages, shrub-grassland and secondary forest, were compared with those of virgin forest. Shrub-grassland had higher herbivore relative abundance but lower fungivore and bacterivore relative abundance than forests. Between secondary and virgin forest, the latter had higher abundance of bacterivores. Shrub-grassland had lower nematode diversity, generic richness, maturity index and trophic diversity index than virgin forest, whereas there were no differences in these indices between secondary forest and virgin forest. The small differences in nematode community structures between secondary forest and virgin forest suggest that soil nematode communities recovered to a level close to that of the undisturbed forest after up to 50 years of natural succession.
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Affiliation(s)
- Yujuan Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200433, P.R. China
- Agri-Science Queensland, Department of Agriculture, Fisheries and Forestry, Leslie Research Centre, 13 Holberton Street, P.O. Box 2282, Toowoomba, QLD 4350, Australia
| | - Guoping Yang
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Deborah A. Neher
- Department of Plant & Soil Science, University of Vermont, Burlington, Vermont 05405, USA
| | - Cheng-Yuan Xu
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
- Faculty of Science, Health, Education and Engineering, the University of the Sunshine Coast, Maroochydore, DC, QLD 4558, Australia
| | - Jihua Wu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200433, P.R. China
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34
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Singh D, Shi L, Adams JM. Bacterial diversity in the mountains of South-West China: climate dominates over soil parameters. J Microbiol 2013; 51:439-47. [PMID: 23990294 DOI: 10.1007/s12275-013-2446-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 03/20/2013] [Indexed: 11/25/2022]
Abstract
Certain patterns in soil bacterial diversity and community composition have become evident from metagenomics studies on a range of scales, from various parts of the world. For example, soil pH has generally been seen as dominating variation in bacterial diversity, above all other soil and climate parameters. It is important however to test the generality of these relationships by studying previously un-sampled areas. We compared soil bacterial diversity and community composition under a wide range of climatic and edaphic conditions in mountainous Yunnan Province, SW China. Soil samples were taken from a range of primary forest types and altitudes, reflecting the great variation of forest environments in this region. From each soil sample, DNA was extracted and pyrosequenced for bacterial 16S rRNA gene identification. In contrast to other recent studies from other parts of the world, pH was a weaker predictor of bacterial community composition and diversity than exchangeable Ca(2+) concentration, and also the more poorly defined environmental parameter of elevation. Samples from within each forest type clustered strongly, showing the distinctive pattern of their microbial communities on a regional scale. It is clear that on a regional scale in a very heterogeneous environment, additional factors beyond pH can emerge as more important in determining bacterial diversity.
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Affiliation(s)
- Dharmesh Singh
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
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35
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Foesel BU, Nägele V, Naether A, Wüst PK, Weinert J, Bonkowski M, Lohaus G, Polle A, Alt F, Oelmann Y, Fischer M, Friedrich MW, Overmann J. Determinants of Acidobacteria activity inferred from the relative abundances of 16S rRNA transcripts in German grassland and forest soils. Environ Microbiol 2013; 16:658-75. [PMID: 23802854 DOI: 10.1111/1462-2920.12162] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Accepted: 05/24/2013] [Indexed: 12/01/2022]
Abstract
16S rRNA genes and transcripts of Acidobacteria were investigated in 57 grassland and forest soils of three different geographic regions. Acidobacteria contributed 9-31% of bacterial 16S rRNA genes whereas the relative abundances of the respective transcripts were 4-16%. The specific cellular 16S rRNA content (determined as molar ratio of rRNA : rRNA genes) ranged between 3 and 80, indicating a low in situ growth rate. Correlations with flagellate numbers, vascular plant diversity and soil respiration suggest that biotic interactions are important determinants of Acidobacteria 16S rRNA transcript abundances in soils. While the phylogenetic composition of Acidobacteria differed significantly between grassland and forest soils, high throughput denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism fingerprinting detected 16S rRNA transcripts of most phylotypes in situ. Partial least squares regression suggested that chemical soil conditions such as pH, total nitrogen, C : N ratio, ammonia concentrations and total phosphorus affect the composition of this active fraction of Acidobacteria. Transcript abundance for individual Acidobacteria phylotypes was found to correlate with particular physicochemical (pH, temperature, nitrogen or phosphorus) and, most notably, biological parameters (respiration rates, abundances of ciliates or amoebae, vascular plant diversity), providing culture-independent evidence for a distinct niche specialization of different Acidobacteria even from the same subdivision.
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Affiliation(s)
- Bärbel U Foesel
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, 82152, Planegg- Martinsried, Germany; Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, 38124, Braunschweig, Germany
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36
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Mumtaz S, Streten-Joyce C, Parry DL, McGuinness KA, Lu P, Gibb KS. Fungi outcompete bacteria under increased uranium concentration in culture media. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2013; 120:39-44. [PMID: 23416228 DOI: 10.1016/j.jenvrad.2013.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 12/19/2012] [Accepted: 01/02/2013] [Indexed: 06/01/2023]
Abstract
As a key part of water management at the Ranger Uranium Mine (Northern Territory, Australia), stockpile (ore and waste) runoff water was applied to natural woodland on the mine lease in accordance with regulatory requirements. Consequently, the soil in these Land Application Areas (LAAs) presents a range of uranium concentrations. Soil samples were collected from LAAs with different concentrations of uranium and extracts were plated onto LB media containing no (0 ppm), low (3 ppm), medium (250 ppm), high (600 ppm) and very high (1500 ppm) uranium concentrations. These concentrations were similar to the range of measured uranium concentrations in the LAAs soils. Bacteria grew on all plates except for the very high uranium concentrations, where only fungi were recovered. Identifications based on bacterial 16S rRNA sequence analysis showed that the dominant cultivable bacteria belonged to the genus Bacillus. Members of the genera Paenibacillus, Lysinibacillus, Klebsiella, Microbacterium and Chryseobacterium were also isolated from the LAAs soil samples. Fungi were identified by sequence analysis of the intergenic spacer region, and members of the genera Aspergillus, Cryptococcus, Penicillium and Curvularia were dominant on plates with very high uranium concentrations. Members of the Paecilomyces and Alternaria were also present but in lower numbers. These findings indicate that fungi can tolerate very high concentrations of uranium and are more resistant than bacteria. Bacteria and fungi isolated at the Ranger LAAs from soils with high concentrations of uranium may have uranium binding capability and hence the potential for uranium bioremediation.
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Affiliation(s)
- Saqib Mumtaz
- Charles Darwin University, Darwin, NT, Australia.
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37
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Turlapati SA, Minocha R, Bhiravarasa PS, Tisa LS, Thomas WK, Minocha SC. Chronic N-amended soils exhibit an altered bacterial community structure in Harvard Forest, MA, USA. FEMS Microbiol Ecol 2012; 83:478-93. [PMID: 22974374 DOI: 10.1111/1574-6941.12009] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 11/28/2022] Open
Abstract
At the Harvard Forest, Petersham, MA, the impact of 20 years of annual ammonium nitrate application to the mixed hardwood stand on soil bacterial communities was studied using 16S rRNA genes pyrosequencing. Amplification of 16S rRNA genes was done using DNA extracted from 30 soil samples (three treatments × two horizons × five subplots) collected from untreated (control), low N-amended (50 kg ha(-1) year(-1)) and high N-amended (150 kg ha(-1) year(-1)) plots. A total of 1.3 million sequences were processed using qiime. Although Acidobacteria represented the most abundant phylum based on the number of sequences, Proteobacteria were the most diverse in terms of operational taxonomic units (OTUs). UniFrac analyses revealed that the bacterial communities differed significantly among soil horizons and treatments. Microsite variability among the five subplots was also evident. Nonmetric multidimensional scaling ordination of normalized OTU data followed by permutational manova further confirmed these observations. Richness indicators and indicator species analyses revealed higher bacterial diversity associated with N amendment. Differences in bacterial diversity and community composition associated with the N treatments were also observed at lower phylogenetic levels. Only 28-35% of the 6 936 total OTUs identified were common to three treatments, while the rest were specific to one treatment or common to two.
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Affiliation(s)
- Swathi A Turlapati
- Department of Biological Sciences, University of New Hampshire, Durham, NH, USA
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38
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Enowashu E, Kandeler E, Schloter M, Rasche F, Engel M. Development of a primer system to study abundance and diversity of the gene coding for alanine aminopeptidase pepN gene in Gram-negative soil bacteria. J Microbiol Methods 2012; 91:14-21. [PMID: 22796679 DOI: 10.1016/j.mimet.2012.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 07/03/2012] [Indexed: 11/27/2022]
Abstract
A new set of primers was developed allowing the specific detection of the pepN gene (coding for alanine aminopeptidase) from Gram-negative bacteria. The primers were designed in silico by sequence alignments based on available DNA sequence data. The PCR assay was validated using DNA from selected pure cultures. The analysis of gene libraries from extracted DNA from different soil samples revealed a high diversity of pepN related sequences mainly related to α-Proteobacteria. Most sequences obtained from clone libraries were closely related to already published sequences (<80% homology on amino acid level), which may be related to the conserved character of the amplified region of pepN. By linking the diversity data obtained by the clone library studies to potential enzymatic activities of alanine aminopeptidase, lowest diversity of pepN was found in those soil samples which displayed lowest activity levels, which confirms the importance of diversity for the ecosystem function mainly when transformation processes of complex molecules are studied.
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Affiliation(s)
- Esther Enowashu
- Institute of Soil Science and Land Evaluation, Soil Biology Section, University of Hohenheim, Emil-Wolf Straße 27, Stuttgart, D-70593, Germany.
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Qi X, Wang E, Xing M, Zhao W, Chen X. Rhizosphere and non-rhizosphere bacterial community composition of the wild medicinal plant Rumex patientia. World J Microbiol Biotechnol 2012; 28:2257-65. [PMID: 22806049 DOI: 10.1007/s11274-012-1033-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Accepted: 02/28/2012] [Indexed: 11/26/2022]
Abstract
To investigate bacterial communities between rhizosphere and non-rhizosphere soils of the wild medicinal plant Rumex patientia of Jilin, China, small subunit rRNAs (16S rDNA) from soil metagenome were amplified by polymerase chain reaction using primers specific to the domain bacteria and analysed by cloning and sequencing. The relative proportion of bacterial communities in rhizosphere soils was similar to non-rhizosphere soils in five phylogenetic groups (Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi and Planctomycetes). But there were differences in five other phylogenetic groups (Firmicutes, Bacteroidetes, Gemmatimonadetes, Verrucomicrobia and Unclassified bacteria). Over 97.24 % of the sequenced clones were found to be unique to rhizosphere and non-rhizosphere soils, while 2.76 % were shared by both of them. Our results indicate that there are differences in the composition and proportion of bacterial communities between rhizosphere and non-rhizosphere soils. Furthermore, the unique bacterial clones between rhizosphere and non-rhizosphere soils of the wild medicinal plant R. patientia have obvious differences.
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Affiliation(s)
- Xiaojuan Qi
- College of Life Science, Jilin University, Changchun 130021, People's Republic of China
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40
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Comparison of bacterial and fungal communities between natural and planted pine forests in subtropical China. Curr Microbiol 2011; 64:34-42. [PMID: 21993713 DOI: 10.1007/s00284-011-0031-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2011] [Accepted: 10/02/2011] [Indexed: 10/16/2022]
Abstract
To improve our understanding of the changes in bacterial and fungal diversity in natural pine and planted forests in subtropical region of China, we examined bacterial and fungal communities from a native and a nearby planted pine forest of the Mt. Lushan by constructing clone libraries of 16S and 18S rRNA genes. For bacterial communities, Proteobacteria and Acidobacteria were dominant bacterial taxa in both two types of forest soils. The Shannon-Wiener diversity index, rarefaction curve analysis, and LibShuff analysis suggest that these two forests contained similar diversity of bacterial communities. Low soil acidity (pH ≈ 4) of our study forests might be one of the most important selection factors determining growth of acidophilic Acidobacteria and Proteobacteria. However, the natural forest harbored greater level of fungal diversity than the planted forest according to the Shannon-Wiener diversity index and rarefaction curve analysis. Basidiomycota and Ascomycota were dominant fungal taxa in the soils of natural and planted forests, respectively. Our results suggest that fungal community was more sensitive than the bacterial community in characterizing the differences in plant cover impacts on the microbial flora in the natural and planted forests. The natural and planted forests may function differently due to the differences in soil fungal diversity and relative abundance.
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41
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Lin YT, Whitman WB, Coleman DC, Chih-Yu C. Molecular characterization of soil bacterial community in a perhumid, low mountain forest. Microbes Environ 2011; 26:325-31. [PMID: 21727759 DOI: 10.1264/jsme2.me11114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Forest disturbance often results in changes in soil properties and microbial communities. In the present study, we characterized a soil bacterial community subjected to disturbance using 16S rRNA gene clone libraries. The community was from a disturbed broad-leaved, low mountain forest ecosystem at Huoshaoliao (HSL) located in northern Taiwan. This locality receives more than 4,000 mm annual precipitation, one of the highest precipitations in Taiwan. Based on the Shannon diversity index, Chao1 estimator, richness and rarefaction curve analysis, the bacterial community in HSL forest soils was more diverse than those previously investigated in natural and disturbed forest soils with colder or less humid weather conditions. Analysis of molecular variance also revealed that the bacterial community in disturbed soils significantly differed from natural forest soils. Most of the abundant operational taxonomic units (OTUs) in the disturbed soil community at HSL were less abundant or absent in other soils. The disturbances influenced the composition of bacterial communities in natural and disturbed forests and increased the diversity of the disturbed forest soil community. Furthermore, the warmer and humid weather conditions could also increase community diversity in HSL soils.
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Affiliation(s)
- Yu-Te Lin
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
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Matsui H, Tsuchiya R, Isobe Y, Narita M. Analysis of bacterial community structure in Saba-Narezushi (Narezushi of Mackerel) by 16S rRNA gene clone library. Journal of Food Science and Technology 2011; 50:791-6. [PMID: 24425983 DOI: 10.1007/s13197-011-0382-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 04/07/2011] [Accepted: 04/12/2011] [Indexed: 11/25/2022]
Abstract
Narezushi, a derivation of sushi, is a traditional Japanese food made by fermenting salted fish meat and cooked rice together. In this study, the microbial diversity of saba-narezushi (narezushi of mackerel, Scomber japonicus) was analyzed by the 16S ribosomal RNA gene clone library method. Chemical composition was also analyzed to compare with different kinds of narezushi. The chemical composition of the narezushi was similar to those obtained from samma-narezushi. Ninety-four clones were randomly selected and DNA sequences of cloned fragments (approx. 890 bp) were analyzed. The DNA sequences obtained were phylogenetically analyzed. The expected operational taxonomy units (OTUs) by Chao1 estimates and Shannon-Wiener index (H') at 97% identity threshold were 48 and 1.822, respectively. The sequence similarity of the cloned fragment was equal to or higher than 98% of the sequence of cultivated bacterial species in the public database. Most of the clones (85%) belonged to lactic acid bacteria (LAB). Lactobacillus curvatus was the most abundant species followed by Lactococcus piscium and Leuconostoc gasicomitatum, suggesting that these bacteria play important roles in the fermentation of saba-narezushi.
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Affiliation(s)
- Hiroki Matsui
- Graduate School of Bioresources, Mie University, Tsu, 514-8507 Japan
| | - Rie Tsuchiya
- Faculty of Education, Mie University, Tsu, 514-8507 Japan
| | - Yuka Isobe
- Faculty of Education, Mie University, Tsu, 514-8507 Japan
| | - Miyo Narita
- Faculty of Education, Mie University, Tsu, 514-8507 Japan
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Lin YT, Jangid K, Whitman WB, Coleman DC, Chiu CY. Change in bacterial community structure in response to disturbance of natural hardwood and secondary coniferous forest soils in central taiwan. MICROBIAL ECOLOGY 2011; 61:429-437. [PMID: 20878522 DOI: 10.1007/s00248-010-9748-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 09/09/2010] [Indexed: 05/29/2023]
Abstract
Forest management often results in changes in the soil and its microbial communities. In the present study, differences in the soil bacterial community caused by forest management practices were characterized using small subunit (SSU) ribosomal RNA (rRNA) gene clone libraries. The communities were from a native hardwood forest (HWD) and two adjacent conifer plantations in a low-elevation montane, subtropical experimental forest at the Lienhuachi Experimental Forest (LHCEF) in central Taiwan. At this locality, the elevation ranges from 600 to 950 m, the mean annual precipitation is 2,200 mm, the mean annual temperature is 20.8 °C, and the soil pH is 4. The conifer forests included a Cunninghamia konishii Hay (CNH) plantation of 40 years and an old growth Calocedrus formosana (Florin) Florin (CLC) forest of 80 years. A total of 476 clones were sequenced and assigned into 12 phylogenetic groups. Proteobacteria-affiliated clones (53%) predominated in the library from HWD soils. In contrast, Acidobacteria was the most abundant phylum and comprised 39% and 57% in the CLC and CNH libraries, respectively. Similarly, the most abundant OTUs in HWD soils were greatly reduced or absent in the CLC and CNH soils. Based on several diversity indices, the numbers of abundant OTUs and singletons, and rarefaction curves, the diversity of the HWD community (0.95 in evenness and Shannon diversity indices) was somewhat less than that in the CNH soils (0.97 in evenness and Shannon diversity indices). The diversity of the community in CLC soils was intermediate. The differences in diversity among the three communities may also reflect changes in abundances of a few OTUs. The CNH forest soil community may be still in a successional phase that is only partially stabilized after 40 years. Analysis of molecular variance also revealed that the bacterial community composition of HWD soils was significantly different from CLC and CNH soils (p = 0.001). These results suggest that the disturbance of forest conversion and tree species composition are important factors influencing the soil bacterial community among three forest ecosystems in the same climate.
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Affiliation(s)
- Yu-Te Lin
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529 Taiwan, Republic of China
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Comparative analysis of acidobacterial genomic fragments from terrestrial and aquatic metagenomic libraries, with emphasis on acidobacteria subdivision 6. Appl Environ Microbiol 2010; 76:6769-77. [PMID: 20729323 DOI: 10.1128/aem.00343-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial phylum Acidobacteria has a widespread distribution and is one of the most common and diverse phyla in soil habitats. However, members of this phylum have often been recalcitrant to cultivation methods, hampering the study of this presumably important bacterial group. In this study, we used a cultivation-independent metagenomic approach to recover genomic information from soilborne members of this phylum. A soil metagenomic fosmid library was screened by PCR targeting acidobacterial 16S rRNA genes, facilitating the recovery of 17 positive clones. Recovered inserts appeared to originate from a range of Acidobacteria subdivisions, with dominance of subdivision 6 (10 clones). Upon full-length insert sequencing, gene annotation identified a total of 350 open reading frames (ORFs), representing a broad range of functions. Remarkably, six inserts from subdivision 6 contained a region of gene synteny, containing genes involved in purine de novo biosynthesis and encoding tRNA synthetase and conserved hypothetical proteins. Similar genomic regions had previously been observed in several environmental clones recovered from soil and marine sediments, facilitating comparisons with respect to gene organization and evolution. Comparative analyses revealed a general dichotomy between marine and terrestrial genes in both phylogeny and G+C content. Although the significance of this homologous gene cluster across subdivision 6 members is not known, it appears to be a common feature within a large percentage of all acidobacterial genomic fragments recovered from both of these environments.
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Bachar A, Al-Ashhab A, Soares MIM, Sklarz MY, Angel R, Ungar ED, Gillor O. Soil microbial abundance and diversity along a low precipitation gradient. MICROBIAL ECOLOGY 2010; 60:453-61. [PMID: 20683588 DOI: 10.1007/s00248-010-9727-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 07/19/2010] [Indexed: 05/22/2023]
Abstract
The exploration of spatial patterns of abundance and diversity patterns along precipitation gradients has focused for centuries on plants and animals; microbial profiles along such gradients are largely unknown. We studied the effects of soil pH, nutrient concentration, salinity, and water content on bacterial abundance and diversity in soils collected from Mediterranean, semi-arid, and arid sites receiving approximately 400, 300, and 100 mm annual precipitation, respectively. Bacterial diversity was evaluated by terminal restriction fragment length polymorphism and clone library analyses and the patterns obtained varied with the climatic regions. Over 75% of the sequenced clones were unique to their environment, while ∼2% were shared by all sites, yet, the Mediterranean and semi-arid sites had more common clones (∼9%) than either had with the arid site (4.7% and 6%, respectively). The microbial abundance, estimated by phospholipid fatty acids and real-time quantitative PCR assays, was significantly lower in the arid region. Our results indicate that although soil bacterial abundance decreases with precipitation, bacterial diversity is independent of precipitation gradient. Furthermore, community composition was found to be unique to each ecosystem.
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Affiliation(s)
- Ami Bachar
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer, 84990 Israel,
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Xie S, Sun W, Luo C, Cupples AM. Novel aerobic benzene degrading microorganisms identified in three soils by stable isotope probing. Biodegradation 2010; 22:71-81. [PMID: 20549308 DOI: 10.1007/s10532-010-9377-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 05/28/2010] [Indexed: 11/26/2022]
Abstract
The remediation of benzene contaminated groundwater often involves biodegradation and although the mechanisms of aerobic benzene biodegradation in laboratory cultures have been well studied, less is known about the microorganisms responsible for benzene degradation in mixed culture samples or at contaminated sites. To address this knowledge gap, DNA based stable isotope probing (SIP) was utilized to identify active benzene degraders in microcosms constructed with soil from three sources (a contaminated site and two agricultural sites). For this, replicate microcosms were amended with either labeled (¹³C) or unlabeled benzene and the extracted DNA samples were ultracentrifuged, fractioned and subject to terminal restriction fragment length polymorphism (TRFLP). The dominant benzene degraders (responsible for ¹³C uptake) were determined by comparing relative abundance of TRFLP phylotypes in heavy fractions of labeled benzene (¹³C) amended samples to the controls (from unlabeled benzene amended samples). Two phylotypes (a Polaromonas sp. and an Acidobacterium) were the major benzene degraders in the microcosms constructed from the contaminated site soil, whereas one phylotype incorporated the majority of the benzene-derived ¹³C in each of the agricultural soils ("candidate" phylum TM7 and an unclassified Sphingomonadaceae).
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Dimitriu PA, Grayston SJ. Relationship between soil properties and patterns of bacterial beta-diversity across reclaimed and natural boreal forest soils. MICROBIAL ECOLOGY 2010; 59:563-573. [PMID: 19830478 DOI: 10.1007/s00248-009-9590-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Accepted: 09/14/2009] [Indexed: 05/28/2023]
Abstract
Productivity gradients in the boreal forest are largely determined by regional-scale changes in soil conditions, and bacterial communities are likely to respond to these changes. Few studies, however, have examined how variation in specific edaphic properties influences the composition of soil bacterial communities along environmental gradients. We quantified bacterial compositional diversity patterns in ten boreal forest sites of contrasting fertility. Bulk soil (organic and mineral horizons) was sampled from sites representing two extremes of a natural moisture-nutrient gradient and two distinct disturbance types, one barren and the other vegetation-rich. We constructed 16S rRNA gene clone libraries to characterize the bacterial communities under phylogenetic- and species-based frameworks. Using a nucleotide analog to label DNA-synthesizing bacteria, we also assessed the composition of active taxa in disturbed sites. Most sites were dominated by sequences related to the alpha-Proteobacteria, followed by acidobacterial and betaproteobacterial sequences. Non-parametric multivariate regression indicated that pH, which was lowest in the natural sites, explained 34% and 16% of the variability in community structure as determined by phylogenetic-based (UniFrac distances) and species-based (Jaccard similarities) metrics, respectively. Soil pH was also a significant predictor of richness (Chao1) and diversity (Shannon) measures. Within the natural edaphic gradient, soil moisture accounted for 32% of the variance in phylogenetic (but not species) community structure. In the boreal system we studied, bacterial beta-diversity patterns appear to be largely related to "master" variables (e.g., pH, moisture) rather than to observable attributes (e.g., plant cover) leading to regional-scale fertility gradients.
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Affiliation(s)
- Pedro A Dimitriu
- Department of Forest Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T1Z4, Canada.
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Matsuzawa H, Tanaka Y, Tamaki H, Kamagata Y, Mori K. Culture-Dependent and Independent Analyses of the Microbial Communities Inhabiting the Giant Duckweed (Spirodela polyrrhiza) Rhizoplane and Isolation of a Variety of Rarely Cultivated Organisms within the Phylum Verrucomicrobia. Microbes Environ 2010; 25:302-8. [DOI: 10.1264/jsme2.me10144] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Hiroaki Matsuzawa
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi
| | - Yasuhiro Tanaka
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
- Research Faculty of Agriculture, Hokkaido University
| | - Kazuhiro Mori
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi
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Zhou J, Huang Y, Mo M. Phylogenetic analysis on the soil bacteria distributed in karst forest. Braz J Microbiol 2009; 40:827-37. [PMID: 24031430 PMCID: PMC3768593 DOI: 10.1590/s1517-838220090004000013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 10/24/2008] [Accepted: 05/15/2009] [Indexed: 12/02/2022] Open
Abstract
Phylogenetic composition of bacterial community in soil of a karst forest was analyzed by culture-independent molecular approach. The bacterial 16S rRNA gene was amplified directly from soil DNA and cloned to generate a library. After screening the clone library by RFLP, 16S rRNA genes of representative clones were sequenced and the bacterial community was analyzed phylogenetically. The 16S rRNA gene inserts of 190 clones randomly selected were analyzed by RFLP and generated 126 different RFLP types. After sequencing, 126 non-chimeric sequences were obtained, generating 113 phylotypes. Phylogenetic analysis revealed that the bacteria distributed in soil of the karst forest included the members assigning into Proteobacteria, Acidobacteria, Planctomycetes, Chloroflexi (Green nonsulfur bacteria), Bacteroidetes, Verrucomicrobia, Nitrospirae, Actinobacteria (High G+C Gram-positive bacteria), Firmicutes (Low G+C Gram-positive bacteria) and candidate divisions (including the SPAM and GN08).
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Affiliation(s)
- Junpei Zhou
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, 650091 , Kunming, P. R. , China
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Ahn JH, Kim YJ, Kim T, Song HG, Kang C, Ka JO. Quantitative improvement of 16S rDNA DGGE analysis for soil bacterial community using real-time PCR. J Microbiol Methods 2009; 78:216-22. [DOI: 10.1016/j.mimet.2009.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2009] [Revised: 06/01/2009] [Accepted: 06/02/2009] [Indexed: 11/24/2022]
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