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Qiang W, Gunina A, Kuzyakov Y, Luo R, Zhang Y, Liu B, Pang X. Shifts of understory vegetation induced by thinning drive the expansion of soil rare fungi. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 342:118119. [PMID: 37207458 DOI: 10.1016/j.jenvman.2023.118119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/21/2023] [Accepted: 05/05/2023] [Indexed: 05/21/2023]
Abstract
The gap formation due to forest thinning regulates the understorey microclimate, ground vegetation, and soil biodiversity. However, little is known about abundant and rare taxa's various patterns and assemblage mechanisms under thinning gaps. Thinning gaps with increasing sizes (0, 74, 109, and 196 m2) were established 12 years ago in a 36-year-old spruce plantation in a temperate mountain climate. Soil fungal and bacterial communities were analyzed by MiSeq sequencing and related to soil physicochemical properties and aboveground vegetation. The functional microbial taxa were sorted by FAPROTAX and Fungi Functional Guild database. The bacterial community stabilized under varied thinning intensities and was not different from the control plots, whereas the richness of the rare fungal taxa was at least 1.5-fold higher in the large gaps than in the small ones. Total phosphorus and dissolved organic carbon were the main factors influencing microbial communities in soil under various thinning gaps. The diversity and richness of the entire fungal community and rare fungal taxa increased with the understorey vegetation coverage and shrub biomass after thinning. Gap formation by thinning stimulated the understorey vegetation, the rare saprotroph (Undefined Saprotroph), and mycorrhizal fungi (Ectomycorrhizal-Endophyte-Ericoid Mycorrhizal-Litter Saprotroph-Orchid Mycorrhizal and Bryophyte Parasite-Lichen Parasite-Ectomycorrhizal-Ericoid Mycorrhizal-Undefined Saprotroph), which may accelerate nutrient cycling in forest ecosystems. However, the abundance of Endophyte-Plant Pathogens increased by eight times, which showed the potential risk for the artificial spruce forests. Thus, fungi may be the driving force of forest restoration and nutrient cycling under the increasing intensity of thinning and may induce plant diseases. Therefore, vegetation coverage and microbial functional diversity should be considered to evaluate the sustainability of the artificial forest ecosystem and forest restoration.
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Affiliation(s)
- Wei Qiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Department of Environmental Chemistry, University of Kassel, Witzenhausen, Germany
| | - Anna Gunina
- Department of Environmental Chemistry, University of Kassel, Witzenhausen, Germany; Department of Soil Biology and Biochemistry, Dokuchaev Soil Science Institute, Russian Federation; Tyumen State University, 625003, Tyumen, Russia
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Goettingen, Göttingen, Germany; Peoples Friendship University of Russia (RUDN University), 117198, Moscow, Russia; Institute of Environmental Sciences, Kazan Federal University, 420049, Kazan, Russia
| | - Ruyi Luo
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China
| | - Yan Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China; Department of Environment and Geography, University of York, Heslington, York, North Yorkshire, UK
| | - Xueyong Pang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China.
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2
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Gurmessa B, Ashworth AJ, Yang Y, Savin M, Moore PA, Ricke SC, Corti G, Pedretti EF, Cocco S. Variations in bacterial community structure and antimicrobial resistance gene abundance in cattle manure and poultry litter. ENVIRONMENTAL RESEARCH 2021; 197:111011. [PMID: 33774017 DOI: 10.1016/j.envres.2021.111011] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/03/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Cattle manure and poultry litter are widely used as fertilizers as they are excellent sources of nutrients; however, potential adverse environmental effects exist during land applications, due to the release of zoonotic bacteria and antimicrobial resistance (AMR) genes. This study was conducted to understand linkages between physiochemical composition, bacterial diversity, and AMR gene presence of cattle manure and poultry litter using quantitative polymerase chain reaction to enumerate four AMR genes (ermB, sulI, intlI, and blactx-m-32), Illumina sequencing of the 16 S region, and analysis of physical and chemical properties. Principal coordinate analysis of Bray-Curtis distance revealed distinct bacterial community structures between the two manure sources. Greater alpha diversity occurred in cattle manure compared to poultry litter (P < 0.05). Redundancy analysis showed a strong relationship between manure physiochemical and composition and bacterial abundance, with positive relationships occurring among electrical conductivity and carbon/nitrogen, and negative associations for total solids and soluble fractions of heavy metals. Cattle manure exhibited greater abundance of macrolide (ermB) and sulfonamide (sulI) resistant genes. Consequently, fresh cattle manure applications may result in greater potential spread of AMR genes to the soil-water environment (relative to poultry litter) and novel best management strategies (such as composting) may reduce the release of AMR genes to the soil-water environment.
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Affiliation(s)
- Biyensa Gurmessa
- Department of Agriculture, Food and Environmental Sciences, Università Politecnica Delle Marche, Via Brecce Bianche 10, 60131, Ancona, Italy
| | - Amanda J Ashworth
- USDA-ARS, Poultry Production and Product Safety Research Unit, 1260 W. Maple St, Fayetteville, AR, 72701, USA.
| | - Yichao Yang
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, 115 Plant Science Building, University of Arkansas, Fayetteville, AR, 72704, USA
| | - Mary Savin
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, 115 Plant Science Building, University of Arkansas, Fayetteville, AR, 72704, USA
| | - Philip A Moore
- USDA-ARS, Poultry Production and Product Safety Research Unit, 1260 W. Maple St, Fayetteville, AR, 72701, USA
| | - Steven C Ricke
- Meat Science & Animal Biologics Discovery Program (MSABD), Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1933 Observatory Drive, Madison, WI, 53706, USA
| | - Giuseppe Corti
- Department of Agriculture, Food and Environmental Sciences, Università Politecnica Delle Marche, Via Brecce Bianche 10, 60131, Ancona, Italy
| | - Ester Foppa Pedretti
- Department of Agriculture, Food and Environmental Sciences, Università Politecnica Delle Marche, Via Brecce Bianche 10, 60131, Ancona, Italy
| | - Stefania Cocco
- Department of Agriculture, Food and Environmental Sciences, Università Politecnica Delle Marche, Via Brecce Bianche 10, 60131, Ancona, Italy
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3
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Pent M, Bahram M, Põldmaa K. Fruitbody chemistry underlies the structure of endofungal bacterial communities across fungal guilds and phylogenetic groups. THE ISME JOURNAL 2020; 14:2131-2141. [PMID: 32409757 PMCID: PMC7368025 DOI: 10.1038/s41396-020-0674-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/29/2020] [Accepted: 04/29/2020] [Indexed: 01/06/2023]
Abstract
Eukaryote-associated microbiomes vary across host taxa and environments but the key factors underlying their diversity and structure in fungi are still poorly understood. Here we determined the structure of bacterial communities in fungal fruitbodies in relation to the main chemical characteristics in ectomycorrhizal (EcM) and saprotrophic (SAP) mushrooms as well as in the surrounding soil. Our analyses revealed significant differences in the structure of endofungal bacterial communities across fungal phylogenetic groups and to a lesser extent across fungal guilds. These variations could be partly ascribed to differences in fruitbody chemistry, particularly the carbon-to-nitrogen ratio and pH. Fungal fruitbodies appear to represent nutrient-rich islands that derive their microbiome largely from the underlying continuous soil environment, with a larger overlap of operational taxonomic units observed between SAP fruitbodies and the surrounding soil, compared with EcM fungi. In addition, bacterial taxa involved in the decomposition of organic material were relatively more abundant in SAP fruitbodies, whereas those involved in release of minerals were relatively more enriched in EcM fruitbodies. Such contrasts in patterns and underlying processes of the microbiome structure between SAP and EcM fungi provide further evidence that bacteria can support the functional roles of these fungi in terrestrial ecosystems.
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Affiliation(s)
- Mari Pent
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411, Tartu, Estonia.
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51, Uppsala, Sweden.
| | - Kadri Põldmaa
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
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Podder A, Reinhart D, Goel R. Integrated leachate management approach incorporating nutrient recovery and removal. WASTE MANAGEMENT (NEW YORK, N.Y.) 2020; 102:420-431. [PMID: 31734553 DOI: 10.1016/j.wasman.2019.10.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 10/23/2019] [Accepted: 10/26/2019] [Indexed: 06/10/2023]
Abstract
This manuscript presents an integrated management scheme for leachate which employed struvite precipitation to recover ammonia nitrogen and phosphorus, aerobic granular sludge process for carbon oxidation (in the form of BOD and sCOD) and single stage anaerobic ammonia oxidation (ANAMMOX) for nitrogen management. The influent fed to the integrated treatment scheme was a mixture of anaerobic digester centrate and real leachate in 4:1 ratio. Almost 77% recovery of phosphorus and 25% removal of NH4+-N were accomplished through struvite precipitation at an optimum pH of 9. High pH contributed to free ammonia loss during struvite precipitation experiments. In the aerobic granular sludge reactor overall, BOD5, COD and NH4+-N removal percentages were 74%, 45% and 35% and in the PN/A reactor, overall 35% removal of total inorganic nitrogen (TIN) was observed. More than 80% BOD removal was recorded in the granular reactor with soluble COD (sCOD) removal fluctuating between 28 and 57% depending on the operational phase. High-throughput amplicon sequencing of 16S rRNA gene targeting V4 region revealed a dominance of phylum Planctomycetes, in the PN/A reactor system. Presence of Rhodobacteraceae, Xanthomonadaceae, Flavobacteriaceae in the granular biomass confirmed the defined redox zones inside mature granules indicating simultaneous removal of nitrogen (N) and organics in aerobic granular sludge technology. Exposing the synthetically cultured aerobic granules directly to the mixture of leachate and centrate unveiled an alteration in physical characteristics of granules; however, reactor operational data and microbial community analysis ascertain the effectiveness of the treatment scheme treating two urban waste-streams.
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Affiliation(s)
- Aditi Podder
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Debra Reinhart
- Department of Civil, Environmental and Construction Engineering, University of Central Florida, Orlando, FL 32816, USA
| | - Ramesh Goel
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT 84112, USA.
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Khan MAW, Bohannan BJM, Nüsslein K, Tiedje JM, Tringe SG, Parlade E, Barberán A, Rodrigues JLM. Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils. FEMS Microbiol Ecol 2019; 95:5211045. [PMID: 30481288 PMCID: PMC6294608 DOI: 10.1093/femsec/fiy230] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/26/2018] [Indexed: 01/28/2023] Open
Abstract
Co-occurrence networks allow for the identification of potential associations among species, which may be important for understanding community assembly and ecosystem functions. We employed this strategy to examine prokaryotic co-occurrence patterns in the Amazon soils and the response of these patterns to land use change to pasture, with the hypothesis that altered microbial composition due to deforestation will mirror the co-occurrence patterns across prokaryotic taxa. In this study, we calculated Spearman correlations between operational taxonomic units (OTUs) as determined by 16S rRNA gene sequencing, and only robust correlations were considered for network construction (-0.80 ≥ P ≥ 0.80, adjusted P < 0.01). The constructed network represents distinct forest and pasture components, with altered compositional and topological features. A comparative analysis between two representative modules of these contrasting ecosystems revealed novel information regarding changes to metabolic pathways related to nitrogen cycling. Our results showed that soil physicochemical properties such as temperature, C/N and H++Al3+ had a significant impact on prokaryotic communities, with alterations to network topologies. Taken together, changes in co-occurrence patterns and physicochemical properties may contribute to ecosystem processes including nitrification and denitrification, two important biogeochemical processes occurring in tropical forest systems.
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Affiliation(s)
- M A Wadud Khan
- Department of Biology, University of Texas, Arlington, TX 76019, USA
| | | | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
| | - Susannah G Tringe
- Joint Genome Institute, United States Department of Energy, Walnut Creek, CA 94598, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eloi Parlade
- Department of Land, Air and Water Resources, University of California - Davis, Davis, CA 95616, USA
| | - Albert Barberán
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ 85721, USA
| | - Jorge L M Rodrigues
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Land, Air and Water Resources, University of California - Davis, Davis, CA 95616, USA
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6
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Yang B, Pang X, Hu B, Bao W, Tian G. Does thinning-induced gap size result in altered soil microbial community in pine plantation in eastern Tibetan Plateau? Ecol Evol 2017; 7:2986-2993. [PMID: 28479998 PMCID: PMC5415508 DOI: 10.1002/ece3.2714] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 12/04/2016] [Accepted: 12/17/2016] [Indexed: 11/10/2022] Open
Abstract
Although the effects of gap formation resulting from thinning on microclimate, plant generation and understory plant community have been well documented, the impact of thinning on soil microbial community and related ecological functions of forests particularly in subalpine coniferous region is largely unknown. Here, the effects of thinning on soil microbial abundance and community structure using phospholipid fatty acid (PLFA) in pine plantations were investigated 6 years after thinning. The experimental treatments consisted of two distinct-sized gaps (30 m2 or 80 m2 in size) resulting from thinning, with closed canopy (free of thinning) as control. Soil temperature as well as the biomass of actinomycete and unspecific bacteria was sensitive to gap formation, but all these variables were only responsive to medium gap. Nonmetric multidimensional scaling confirmed that soil microbial community was responsive to gap size. In addition, gap size exerted contrasting effect on bacteria-feeding nematode and fungi-feeding nematodes. In conclusion, thinning-induced gap size would affect soil microbial community through changing soil temperature or the abundance of fungi-feeding nematodes.
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Affiliation(s)
- Bing Yang
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province Chengdu Institute of Biology Chinese Academy of Sciences Chengdu China
| | - Xueyong Pang
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province Chengdu Institute of Biology Chinese Academy of Sciences Chengdu China
| | - Bin Hu
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province Chengdu Institute of Biology Chinese Academy of Sciences Chengdu China
| | - Weikai Bao
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province Chengdu Institute of Biology Chinese Academy of Sciences Chengdu China
| | - Guanglong Tian
- Environmental Monitoring and Research Division Monitoring and Research Department Metropolitan Water Reclamation District of Greater Chicago Cicero IL USA.,Department of Civil, Architectural & Environmental Engineering Illinois Institute of Technology Chicago IL USA
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7
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Anas A, Nilayangod C, Jasmin C, Vinothkumar S, Parameswaran PS, Nair S. Diversity and bioactive potentials of culturable heterotrophic bacteria from the surficial sediments of the Arabian Sea. 3 Biotech 2016; 6:238. [PMID: 28330310 PMCID: PMC5106401 DOI: 10.1007/s13205-016-0556-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/19/2016] [Indexed: 11/28/2022] Open
Abstract
Marine sediments accommodate plethora of diverse microorganisms with varying ecological functions. In the present study, we isolated bacteria from surficial sediments of south east Arabian Sea (AS) and evaluated their bioactive potentials. A total of 131 isolates belonging to the phylum: γ-Proteobacteria (63%), Bacillales (34%) and Micrococcaceae (3%) were isolated. Among these, about 40% of the isolates showed the presence of secondary metabolite biosynthetic genes such as PKS or NRPS or both. Organic extracts of nearly 50% of these organisms were cytotoxic to human breast cancer MCF-7 cells and were bactericidal to human pathogens, Escherichia coli and Pseudomonas sp., while 20–30% of them were bactericidal to Vibrio sp. and Staphylococcus sp. too. In all, 8 isolates, belonging to Pseudomonas spp., Bacillus sp. and/or Lysinibacillus sp. displayed high level of bactericidal/cytotoxic properties. The study proposes AS sediment as a rich source for microorganisms with prospective bioactive molecules.
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Affiliation(s)
- Abdulaziz Anas
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India.
| | - Charulatha Nilayangod
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India
| | - C Jasmin
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India
| | - Saradavey Vinothkumar
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India
| | - P S Parameswaran
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India
| | - Shanta Nair
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India
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Huang R, Zhao D, Zeng J, Shen F, Cao X, Jiang C, Huang F, Feng J, Yu Z, Wu QL. pH affects bacterial community composition in soils across the Huashan Watershed, China. Can J Microbiol 2016; 62:726-34. [PMID: 27374919 DOI: 10.1139/cjm-2015-0783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To investigate soil bacterial richness and diversity and to determine the correlations between bacterial communities and soil properties, 8 soil samples were collected from the Huashan watershed in Anhui, China. Subsequently, 454 high-throughput pyrosequencing and bioinformatics analyses were performed to examine the soil bacterial community compositions. The operational taxonomic unit richness of the bacterial community ranged from 3664 to 5899, and the diversity indices, including Chao1, Shannon-Wiener, and Faith's phylogenetic diversity ranged from 7751 to 15 204, 7.386 to 8.327, and 415.77 to 679.11, respectively. The 2 most dominant phyla in the soil samples were Actinobacteria and Proteobacteria. The richness and diversity of the bacterial community were positively correlated with soil pH. The Mantel test revealed that the soil pH was the dominant factor influencing the bacterial community. The positive modular structure of co-occurrence patterns at the genus level was discovered by network analysis. The results obtained in this study provide useful information that enhances our understanding of the effects of soil properties on the bacterial communities.
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Affiliation(s)
- Rui Huang
- a State Key Laboratory of Hydrology - Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China.,b College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China.,c State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Dayong Zhao
- a State Key Laboratory of Hydrology - Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China.,b College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Jin Zeng
- c State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Feng Shen
- a State Key Laboratory of Hydrology - Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China.,b College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China.,c State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xinyi Cao
- a State Key Laboratory of Hydrology - Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China.,b College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Cuiling Jiang
- b College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Feng Huang
- b College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Jingwei Feng
- d School of Civil Engineering, Hefei University of Technology, Hefei 230009, China
| | - Zhongbo Yu
- a State Key Laboratory of Hydrology - Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China.,b College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Qinglong L Wu
- c State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
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Zhang X, Xu S, Li C, Zhao L, Feng H, Yue G, Ren Z, Cheng G. The soil carbon/nitrogen ratio and moisture affect microbial community structures in alkaline permafrost-affected soils with different vegetation types on the Tibetan plateau. Res Microbiol 2014; 165:128-39. [DOI: 10.1016/j.resmic.2014.01.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 01/04/2014] [Indexed: 11/27/2022]
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10
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Zhang XF, Zhao L, Xu SJ, Liu YZ, Liu HY, Cheng GD. Soil moisture effect on bacterial and fungal community in Beilu River (Tibetan Plateau) permafrost soils with different vegetation types. J Appl Microbiol 2013; 114:1054-65. [PMID: 23241008 DOI: 10.1111/jam.12106] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 12/07/2012] [Accepted: 12/07/2012] [Indexed: 11/29/2022]
Abstract
AIM This study investigated the effects of environmental variables on the bacterial and fungal communities of the Beilu River (on the Tibetan Plateau) permafrost soils with different vegetation types. METHODS AND RESULTS Microbial communities were sampled from meadow, steppe and desert steppe permafrost soils during May, June, August and November, and they were analysed by both pyrosequencing and the use of Biolog EcoPlates. The dominant bacterial and fungal phyla in meadow and steppe soils were Proteobacteria and Ascomycota, whereas Actinobacteria and Basidiomycota predominated in desert steppe soils. The bacterial communities in meadow soils degraded amines and amino acids very rapidly, while polymers were degraded rapidly by steppe communities. The RDA patterns showed that the microbial communities differed greatly between meadow, steppe and desert steppe, and they were related to variations in the soil moisture, C/N ratio and pH. A UniFrac analysis detected clear differences between the desert steppe bacterial community and others, and seasonal shifts were observed. The fungal UniFrac patterns differed significantly between meadow and steppe soils. There were significant correlations between the bacterial diversity (H') and soil moisture (r = 0.506) and C/N (r = 0.527). The fungal diversity (Hf') was significantly correlated with the soil pH (r = 0.541). CONCLUSION The soil moisture, C/N ratio and pH were important determinants of the microbial community structure in Beilu River permafrost soils. SIGNIFICANCE AND IMPACT OF THE STUDY These results may provide a useful baseline for predicting the variation in microbial communities in response to climate changes.
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Affiliation(s)
- X F Zhang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
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11
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Assessing the Environmental Benefits of Compost Use-on-Land through an LCA Perspective. SUSTAINABLE AGRICULTURE REVIEWS 2013. [DOI: 10.1007/978-94-007-5961-9_9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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12
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Assessing the microbial community and functional genes in a vertical soil profile with long-term arsenic contamination. PLoS One 2012; 7:e50507. [PMID: 23226297 PMCID: PMC3511582 DOI: 10.1371/journal.pone.0050507] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 10/22/2012] [Indexed: 11/19/2022] Open
Abstract
Arsenic (As) contamination in soil and groundwater has become a serious problem to public health. To examine how microbial communities and functional genes respond to long-term arsenic contamination in vertical soil profile, soil samples were collected from the surface to the depth of 4 m (with an interval of 1 m) after 16-year arsenic downward infiltration. Integrating BioLog and functional gene microarray (GeoChip 3.0) technologies, we showed that microbial metabolic potential and diversity substantially decreased, and community structure was markedly distinct along the depth. Variations in microbial community functional genes, including genes responsible for As resistance, carbon and nitrogen cycling, phosphorus utilization and cytochrome c oxidases were detected. In particular, changes in community structures and activities were correlated with the biogeochemical features along the vertical soil profile when using the rbcL and nifH genes as biomarkers, evident for a gradual transition from aerobic to anaerobic lifestyles. The C/N showed marginally significant correlations with arsenic resistance (p = 0.069) and carbon cycling genes (p = 0.073), and significant correlation with nitrogen fixation genes (p = 0.024). The combination of C/N, NO3− and P showed the highest correlation (r = 0.779, p = 0.062) with the microbial community structure. Contradict to our hypotheses, a long-term arsenic downward infiltration was not the primary factor, while the spatial isolation and nutrient availability were the key forces in shaping the community structure. This study provides new insights about the heterogeneity of microbial community metabolic potential and future biodiversity preservation for arsenic bioremediation management.
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Bao Z, Ikunaga Y, Matsushita Y, Morimoto S, Takada-Hoshino Y, Okada H, Oba H, Takemoto S, Niwa S, Ohigashi K, Suzuki C, Nagaoka K, Takenaka M, Urashima Y, Sekiguchi H, Kushida A, Toyota K, Saito M, Tsushima S. Combined analyses of bacterial, fungal and nematode communities in andosolic agricultural soils in Japan. Microbes Environ 2012; 27:72-9. [PMID: 22223474 PMCID: PMC4036027 DOI: 10.1264/jsme2.me11281] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
We simultaneously examined the bacteria, fungi and nematode communities in Andosols from four agro-geographical sites in Japan using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and statistical analyses to test the effects of environmental factors including soil properties on these communities depending on geographical sites. Statistical analyses such as Principal component analysis (PCA) and Redundancy analysis (RDA) revealed that the compositions of the three soil biota communities were strongly affected by geographical sites, which were in turn strongly associated with soil characteristics such as total C (TC), total N (TN), C/N ratio and annual mean soil temperature (ST). In particular, the TC, TN and C/N ratio had stronger effects on bacterial and fungal communities than on the nematode community. Additionally, two-way cluster analysis using the combined DGGE profile also indicated that all soil samples were classified into four clusters corresponding to the four sites, showing high site specificity of soil samples, and all DNA bands were classified into four clusters, showing the coexistence of specific DGGE bands of bacteria, fungi and nematodes in Andosol fields. The results of this study suggest that geography relative to soil properties has a simultaneous impact on soil microbial and nematode community compositions. This is the first combined profile analysis of bacteria, fungi and nematodes at different sites with agricultural Andosols.
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Affiliation(s)
- Zhihua Bao
- National Institute for Agro-Environmental Sciences, Tsukuba, Japan
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14
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Cao ZJ, Lu D, Luo LS, Deng YX, Bian YG, Zhang XQ, Zhou MH. Composition analysis and application of degradation products of whole feathers through a large scale of fermentation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2011; 19:2690-2696. [PMID: 22293907 DOI: 10.1007/s11356-012-0763-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 01/13/2012] [Indexed: 05/31/2023]
Abstract
PURPOSE Feathers are one of the most abundant bioresources. They are discarded as waste in most cases and could cause environmental pollution. On the other hand, keratin constituted by amino acids is the main component of feathers. In this article, we reported on biorefined feathers and integrants and application of degraded products. MATERIALS AND METHODS The fermentation of whole chicken feathers with Stenotrophomonas maltophilia DHHJ in a scale-up of a 5-L bioreactor was investigated in this article. The fermentation process was controlled at 0.08 MPa pressure, 2.5 L/min airflow, and 300 rpm as 100% oxygen saturation level, 40°C, and pH 7.8. RESULTS Feathers were almost completely degraded in the tested fermentation reaction with the following conditions: 80 g of whole feathers in 3 L fermentation broth for 72 h, seed age of 16 h, 100 mL inoculation amount, and 50% oxygen saturation level. The degraded products contain 397.1 mg/L soluble protein that has mass weight ranging from 10 to 160 kD, 336.9 mg/L amino acids, and many kinds of metal ions. The fermentation broth was evaluated as leaf fertilizer and found to increase plant growth to 82% or 66% for two- or fourfold dilutions, respectively. In addition, in a hair care assay, the broth showed a hair protective function by increasing weight, flexibility, and strength of the treated hair. CONCLUSIONS The whole feathers were degraded completely by S. maltophilia DHHJ. The degraded product includes many factors to life, such as peptides, amino acids, and mineral elements. It could be applied as leaf fertilizer and hair care product.
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Affiliation(s)
- Zhang-Jun Cao
- Key Laboratory of Science & Technology of Eco-Textile, Donghua University, Ministry of Education, Shanghai 201620, China
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The spatial factor, rather than elevated CO₂, controls the soil bacterial community in a temperate Forest Ecosystem. Appl Environ Microbiol 2010; 76:7429-36. [PMID: 20851972 DOI: 10.1128/aem.00831-10] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The global atmospheric carbon dioxide (CO₂) concentration is expected to increase continuously over the next century. However, little is known about the responses of soil bacterial communities to elevated CO₂ in terrestrial ecosystems. This study aimed to partition the relative influences of CO₂, nitrogen (N), and the spatial factor (different sampling plots) on soil bacterial communities at the free-air CO₂ enrichment research site in Duke Forest, North Carolina, by two independent techniques: an entirely sequencing-based approach and denaturing gradient gel electrophoresis. Multivariate regression tree analysis demonstrated that the spatial factor could explain more than 70% of the variation in soil bacterial diversity and 20% of the variation in community structure, while CO₂ or N treatment explains less than 3% of the variation. For the effects of soil environmental heterogeneity, the diversity estimates were distinguished mainly by the total soil N and C/N ratio. Bacterial diversity estimates were positively correlated with total soil N and negatively correlated with C/N ratio. There was no correlation between the overall bacterial community structures and the soil properties investigated. This study contributes to the information about the effects of elevated CO₂ and soil fertility on soil bacterial communities and the environmental factors shaping the distribution patterns of bacterial community diversity and structure in temperate forest soils.
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