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Trofymow JA, Shay PE, Tomm B, Bérubé JA, Ramsfield T. Differences in Soil Fungal Communities between Forested Reclamation and Forestry Sites in the Alberta Oil Sands Region. J Fungi (Basel) 2023; 9:1110. [PMID: 37998915 PMCID: PMC10672713 DOI: 10.3390/jof9111110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Fungi play key roles in forest soils and provide benefits to trees via mycorrhizal symbioses. After severe disturbance, forest regrowth can be impeded because of changes in fungal communities. In 2013-2014, soil fungi in forest floor and mineral soil were examined by Roche 454 pyrosequencing in undisturbed, harvested, and burned jack pine stands in a forested area near Fort Chipewyan, Alberta. These fungal communities were compared with jack pine, white spruce, and larch stands in Gateway Hill, a nearby certified reclaimed area. In 2014, a more detailed sampling of forestry and reclamation jack pine sites examined fungi in soil fractions using two high-throughput sequencing platforms and a sporocarp survey. The significances of compositional and functional differences in fungal communities between the forested and reclamation sites were assessed using permutation tests of partially constrained ordinations, accounting for confounding factors by variance partitioning. Taxa associated with the forestry area were primarily ectomycorrhizal. Fungal richness and diversity were greater in soils from the reclamation sites and included significantly more pathogenic taxa and taxa with unknown functional properties. Fungal community dissimilarities may have been artefacts of historical legacies or, alternatively, may have resulted from contrasting niche differentiation between forestry and reclamation sites.
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Affiliation(s)
- John. A. Trofymow
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
| | - Philip-Edouard Shay
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
- Canadian Wood Fibre Centre, Canadian Forest Service, 1350 Regent Street, Fredericton, NB E3B 5P7, Canada;
| | - Bradley Tomm
- Northern Forestry Centre, Canadian Forest Service, Natural Resources Canada, 5320-122nd Street, Edmonton, AB T6H 3S5, Canada; (B.T.); (T.R.)
| | - Jean A. Bérubé
- Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, 1055 Rue du Peps, Québec, QC G1V 4C7, Canada;
| | - Tod Ramsfield
- Northern Forestry Centre, Canadian Forest Service, Natural Resources Canada, 5320-122nd Street, Edmonton, AB T6H 3S5, Canada; (B.T.); (T.R.)
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Shay PE, Winder RS, Constabel CP, Trofymow JA(T. Fungal Community Composition as Affected by Litter Chemistry and Weather during Four Years of Litter Decomposition in Rainshadow Coastal Douglas-Fir Forests. J Fungi (Basel) 2022; 8:jof8070735. [PMID: 35887490 PMCID: PMC9323820 DOI: 10.3390/jof8070735] [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: 05/21/2022] [Revised: 07/07/2022] [Accepted: 07/13/2022] [Indexed: 12/04/2022] Open
Abstract
Climate and litter chemistry are major factors influencing litter decay, a process mediated by microbes, such as fungi, nitrogen-fixing bacteria and ammonia-oxidizing bacteria. Increasing atmospheric CO2 concentrations can decrease nitrogen (N) and increase condensed tannin (CT) content in foliar litter, reducing litter quality and slowing decomposition. We hypothesized that reduced litter quality inhibits microbes and is the mechanism causing decomposition to slow. Litterbags of Douglas-fir needles and poplar leaves with a range of N (0.61–1.57%) and CT (2.1–29.1%) treatment and natural acid unhydrolyzable residue (35.3–41.5%) concentrations were placed along climatic gradients in mature Douglas-fir stands of coastal British Columbia rainshadow forests. The structure (diversity, richness and evenness) and composition of microbial communities were analyzed using DGGE profiles of 18S, NifH-universal and AmoA PCR amplicons in foliar litter after 7, 12, 24 and 43 months of decay. High CT and low N concentrations in leaf litter were associated with changes in microbial community composition, especially fungi. Contrary to our hypothesis, high CT and low N treatments did not inhibit microbial colonization or diversity. The joint effects of air temperature and soil moisture on microbial community composition at our sites were more important than the effects of initial litter chemistry.
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Affiliation(s)
- Philip-Edouard Shay
- Centre for Forest Biology, Department of Biology, University of Victoria, Victoria, BC V8W 3N5, Canada; (P.-E.S.); (C.P.C.)
- Pacific Forestry Centre, Canadian Forest Service, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada;
| | - Richard S. Winder
- Pacific Forestry Centre, Canadian Forest Service, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada;
| | - C. Peter Constabel
- Centre for Forest Biology, Department of Biology, University of Victoria, Victoria, BC V8W 3N5, Canada; (P.-E.S.); (C.P.C.)
| | - J. A. (Tony) Trofymow
- Centre for Forest Biology, Department of Biology, University of Victoria, Victoria, BC V8W 3N5, Canada; (P.-E.S.); (C.P.C.)
- Pacific Forestry Centre, Canadian Forest Service, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada;
- Correspondence:
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Alem D, Dejene T, Geml J, Oria-de-Rueda JA, Martín-Pinto P. Metabarcoding analysis of the soil fungal community to aid the conservation of underexplored church forests in Ethiopia. Sci Rep 2022; 12:4817. [PMID: 35314738 PMCID: PMC8938458 DOI: 10.1038/s41598-022-08828-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 03/14/2022] [Indexed: 11/10/2022] Open
Abstract
Most of the Dry Afromontane forests in the northern part of Ethiopia are located around church territories and, hence, are called church forests. These forests are biodiversity islands and provide key ecosystem services to local communities. A previous study of church forest fungal species was based on sporocarp collections. However, to obtain a complete picture of the fungal community, the total fungal community present in the soil needs to be analyzed. This information is important to integrate church forests into global biodiversity conservation strategies and to understand what actions are required to conserve church forests and their biological components, including fungi, which are known for their exceptionally high diversity levels. We assessed soil fungal communities in three church forests using ITS2 rDNA metabarcoding. In total, 5152 fungal operational taxonomic units representing 16 fungal phyla were identified. Saprotrophs followed by ectomycorrhizal fungi and animal pathogens dominated fungal communities. Significant differences in diversity and richness were observed between forests. Non-metric multidimensional scaling confirmed that fungal community composition differed in each forest. The composition was influenced by climatic, edaphic, vegetation, and spatial variables. Linear relationships were found between tree basal area and the abundance of total fungi and trophic groups. Forest management strategies that consider cover, tree density, enrichment plantations of indigenous host tree species, and environmental factors would offer suitable habitats for fungal diversity, production, and function in these forest systems. The application of the baseline information obtained in this study could assist other countries with similar forest conservation issues due to deforestation and forest fragmentation.
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Affiliation(s)
- Demelash Alem
- Sustainable Forest Management Research Institute, University of Valladolid, Avda. Madrid 44, 34071, Palencia, Spain.,Ethiopian Environment and Forest Research Institute (EEFRI), P. O. Box 30708, 1000, Addis Ababa, Ethiopia
| | - Tatek Dejene
- Sustainable Forest Management Research Institute, University of Valladolid, Avda. Madrid 44, 34071, Palencia, Spain.,Ethiopian Environment and Forest Research Institute (EEFRI), P. O. Box 30708, 1000, Addis Ababa, Ethiopia
| | - József Geml
- MTA-EKE Lendület Environmental Microbiome Research Group, Eszterházy Károly University, Leányka u. 6, 3300, Eger, Hungary
| | - Juan Andrés Oria-de-Rueda
- Sustainable Forest Management Research Institute, University of Valladolid, Avda. Madrid 44, 34071, Palencia, Spain
| | - Pablo Martín-Pinto
- Sustainable Forest Management Research Institute, University of Valladolid, Avda. Madrid 44, 34071, Palencia, Spain.
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Ji RQ, Xie ML, Li GL, Xu Y, Gao TT, Xing PJ, Meng LP, Liu SY. Response of bacterial community structure to different ecological niches and their functions in Korean pine forests. PeerJ 2022; 10:e12978. [PMID: 35251783 PMCID: PMC8893031 DOI: 10.7717/peerj.12978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 01/31/2022] [Indexed: 01/11/2023] Open
Abstract
A healthy plant microbiome is diverse, taxonomically-structured, and gives its plant host moderate advantages in growth, development, stress tolerance, and disease resistance. The plant microbiome varies with ecological niches and is influenced by variables that are complex and difficult to separate from each other, such as the plant species, soil, and environmental factors. To explore the composition, diversity, and functions of the bacterial community of Korean pine forests, we used high-throughput sequencing to study five areas with different forest ages from June to October 2017 in northeast China. We obtained 3,247 operational taxonomic units (OTUs) based on 16S rRNA gene sequencing via an Illumina Hi-seq platform. A total of 36 phyla and 159 known genera were classified. The Shannon index of the bacterial community from the rhizospheric soil was significantly higher (p < 0.01, n = 10) than that of the root tips. Beta-diversity analysis confirmed that the bacterial community of the rhizospheric soil was significantly different (p < 0.001) from the root tips. Nine bacterial phyla were dominant (relative richness > 1%) in the rhizospheric soil, but there were six dominant phyla in the root tips. Proteobacteria was the core flora in the root tips with a relative abundance of more than 50%. It is known that the formation of bacterial communities in the rhizospheric soil or the root is mainly caused by the processes of selection, and we found a relatively high abundance of a few dominant species. We further analyzed the correlations between the bacterial community from the rhizospheric soil with that of the root tips, as well as the correlations of the bacterial community with soil physicochemical properties and climate factors. We used Functional Annotation of the Prokaryotic Tax (FAPROTAX) to predict the functions of the bacterial community in the rhizospheric soil and root tips. Five related phototrophic functions, nine nitrogen cycle functions, two related chemoheterotrophic functions, and two others were predicted. The abundance of the bacteria phyla performing relevant functions was different in the rhizospheric soil than in the root tips. These functions were significantly influenced by the contents of nitrogen, phosphorus, and potassium in the soil habitat. The bacterial composition and functions in the rhizospheric soil and root tips of Korean pine were analyzed, and the results demonstrated the importance of soil and plant species on the bacterial community in the below ground plant microbiome.
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Affiliation(s)
- Rui-Qing Ji
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, Jilin Province, China,Key Laboratory of Edible Fungus Resources Utilization in North China, Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun, Jilin Province, China
| | - Meng-Le Xie
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, Jilin Province, China,Life Science College, Northeast Normal University, Changchun, Jilin Province, China
| | - Guan-Lin Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, Jilin Province, China
| | - Yang Xu
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, Jilin Province, China
| | - Ting-Ting Gao
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, Jilin Province, China
| | - Peng-Jie Xing
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, Jilin Province, China
| | - Li-Peng Meng
- Wood Research Institute, Jilin Forestry Science Institute, Changchun, Jilin Province, China
| | - Shu-Yan Liu
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, Jilin Province, China
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Diazotrophs Show Signs of Restoration in Amazon Rain Forest Soils with Ecosystem Rehabilitation. Appl Environ Microbiol 2020; 86:AEM.00195-20. [PMID: 32169937 DOI: 10.1128/aem.00195-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/08/2020] [Indexed: 11/20/2022] Open
Abstract
Biological nitrogen fixation can be an important source of nitrogen in tropical forests that serve as a major CO2 sink. Extensive deforestation of the Amazon is known to influence microbial communities and the biogeochemical cycles they mediate. However, it is unknown how diazotrophs (nitrogen-fixing microorganisms) respond to deforestation and subsequent ecosystem conversion to agriculture, as well as whether they can recover in secondary forests that are established after agriculture is abandoned. To address these knowledge gaps, we combined a spatially explicit sampling approach with high-throughput sequencing of nifH genes. The main objectives were to assess the functional distance decay relationship of the diazotrophic bacterial community in a tropical forest ecosystem and to quantify the roles of various factors that drive the observed changes in the diazotrophic community structure. We observed an increase in local diazotrophic diversity (α-diversity) with a decrease in community turnover (β-diversity), associated with a shift in diazotrophic community structure as a result of the forest-to-pasture conversion. Both diazotrophic community turnover and structure showed signs of recovery in secondary forests. Changes in the diazotrophic community were primarily driven by the change in land use rather than differences in geochemical characteristics or geographic distances. The diazotroph communities in secondary forests resembled those in primary forests, suggesting that at least partial recovery of diazotrophs is possible following agricultural abandonment.IMPORTANCE The Amazon region is a major tropical forest region that is being deforested at an alarming rate to create space for cattle ranching and agriculture. Diazotrophs (nitrogen-fixing microorganisms) play an important role in supplying soil N for plant growth in tropical forests. It is unknown how diazotrophs respond to deforestation and whether they can recover in secondary forests that establish after agriculture is abandoned. Using high-throughput sequencing of nifH genes, we characterized the response of diazotrophs' β-diversity and identified major drivers of changes in diazotrophs from forest-to-pasture and pasture-to-secondary-forest conversions. Studying the impact of land use change on diazotrophs is important for a better understanding of the impact of deforestation on tropical forest ecosystem functioning, and our results on the potential recovery of diazotrophs in secondary forests imply the possible restoration of ecosystem functions in secondary forests.
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Distance from the Forest Edge Influences Soil Fungal Communities Colonizing a Reclaimed Soil Borrow Site in Boreal Mixedwood Forest. FORESTS 2020. [DOI: 10.3390/f11040427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Soil fungi are important components of boreal forest ecosystems; for example, saprotrophic fungi regulate nutrient cycling, and mycorrhizal species facilitate nutrient uptake by plants. This study aimed to assess soil fungal communities in a reclaimed area and an adjacent natural mixedwood forest and to identify the distribution of taxa available for seedling colonization. Soil fungal microbiomes were assessed along three transects (from 10 m inside the interior of the undisturbed forest to 40 m inside the reclaimed area) and in the roots of small aspen within the natural forest. Using high-throughput deoxyribonucleic acid (DNA) sequencing of internal transcribed spacer amplicons, a total of 2796 unique fungal taxa were detected across fine roots, forest floor, and mineral soils collected along the transects, whereas 166 taxa were detected in the aspen roots from the natural forest. Within the interior of the forest, ectomycorrhizal fungi were more common, whereas in the reclaimed areas, arbuscular mycorrhizae and saprophytes were more common. This survey showed that natural areas of adjacent undisturbed forest can act as a source of ectomycorrhizal fungi for dispersal into reclaimed areas. Notably, soil fungal taxa colonizing the root systems of small aspen included species that are specifically associated with soils from the undisturbed forest (primarily ectomycorrhizae) or the reclaimed clearing (saprotrophs and plant pathogens).
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Qin H, Wang S, Feng K, He Z, Virta MPJ, Hou W, Dong H, Deng Y. Unraveling the diversity of sedimentary sulfate-reducing prokaryotes (SRP) across Tibetan saline lakes using epicPCR. MICROBIOME 2019; 7:71. [PMID: 31054577 PMCID: PMC6500586 DOI: 10.1186/s40168-019-0688-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/25/2019] [Indexed: 05/07/2023]
Abstract
Sulfate reduction is an important biogeochemical process in the ecosphere; however, the major taxa of sulfate reducers have not been fully identified. Here, we used epicPCR (Emulsion, Paired Isolation, and Concatenation PCR) technology to identify the phylogeny of sulfate-reducing prokaryotes (SRP) in sediments from Tibetan Plateau saline lakes. A total of 12,519 OTUs and 883 SRP-OTUs were detected in ten lakes by sequencing of 16S rRNA gene PCR amplicons and epicPCR products of fused 16S rRNA plus dsrB gene, respectively, with Proteobacteria, Firmicutes, and Bacteroidetes being the dominant phyla in both datasets. The 120 highly abundant SRP-OTUs (> 1% in at least one sample) were affiliated with 17 described phyla, only 7 of which are widely recognized as SRP phyla. The majority of OTUs from both the whole microbial communities and the SRPs were not detected in more than one specific lake, suggesting high levels of endemism. The α-diversity of the entire microbial community and SRP sub-community showed significant positive correlations. The pH value and mean water temperature of the month prior to sampling were the environmental determinants for the whole microbial community, while the mean water temperature and total nitrogen were the major environmental drivers for the SRP sub-community. This study revealed there are still many undocumented SRP in Tibetan saline lakes, many of which could be endemic and adapted to specific environmental conditions.
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Affiliation(s)
- Huayu Qin
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shang Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhili He
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Marko P J Virta
- Department of Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, United States
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Rd, Haidian, Beijing, 100085, China.
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Che R, Deng Y, Wang F, Wang W, Xu Z, Hao Y, Xue K, Zhang B, Tang L, Zhou H, Cui X. Autotrophic and symbiotic diazotrophs dominate nitrogen-fixing communities in Tibetan grassland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 639:997-1006. [PMID: 29929338 DOI: 10.1016/j.scitotenv.2018.05.238] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/16/2018] [Accepted: 05/19/2018] [Indexed: 06/08/2023]
Abstract
Biological nitrogen fixation, conducted by soil diazotrophs, is the primary nitrogen source for natural grasslands. However, the diazotrophs in grassland soils are still far from fully investigated. Particularly, their regional-scale distribution patterns have never been systematically examined. Here, soils (0-5 cm) were sampled from 54 grasslands on the Tibetan Plateau to examine the diazotroph abundance, diversity, and community composition, as well as their distribution patterns and driving factors. The diazotroph abundance was expressed as nifH gene copies, measured using real-time PCR. The diversity and community composition of diazotrophs were analyzed through MiSeq sequencing of nifH genes. The results showed that Cyanobacteria (47.94%) and Proteobacteria (45.20%) dominated the soil diazotroph communities. Most Cyanobacteria were classified as Nostocales which are main components of biological crusts. Rhizobiales, most of which were identified as potential symbiotic diazotrophs, were also abundant in approximately half of the soil samples. The soil diazotroph abundance, diversity, and community composition followed the distribution patterns in line with mean annual precipitation. Moreover, they also showed significant correlations with prokaryotic abundance, plant biomass, vegetation cover, soil pH values, and soil nutrient contents. Among these environmental factors, the soil moisture, organic carbon, available phosphorus, and inorganic nitrogen contents could be the main drivers of diazotroph distribution due to their strong correlations with diazotroph indices. These findings suggest that autotrophic and symbiotic diazotrophs are the predominant nitrogen fixers in Tibetan grassland soils, and highlight the key roles of water and nutrient availability in determining the soil diazotroph distribution on the Tibetan Plateau.
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Affiliation(s)
- Rongxiao Che
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Yongcui Deng
- Nanjing Normal University, Nanjing 210097, China; Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing 210023, China
| | - Fang Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Weijin Wang
- Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Zhihong Xu
- Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Yanbin Hao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Xue
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Biao Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Tang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Huakun Zhou
- Key Laboratory of Restoration Ecology of Cold Area in Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Xiaoyong Cui
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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Du B, Kreuzwieser J, Dannenmann M, Junker LV, Kleiber A, Hess M, Jansen K, Eiblmeier M, Gessler A, Kohnle U, Ensminger I, Rennenberg H, Wildhagen H. Foliar nitrogen metabolism of adult Douglas-fir trees is affected by soil water availability and varies little among provenances. PLoS One 2018; 13:e0194684. [PMID: 29566035 PMCID: PMC5864041 DOI: 10.1371/journal.pone.0194684] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 03/07/2018] [Indexed: 12/29/2022] Open
Abstract
The coniferous forest tree Douglas-fir (Pseudotsuga menziesii) is native to the pacific North America, and is increasingly planted in temperate regions worldwide. Nitrogen (N) metabolism is of great importance for growth, resistance and resilience of trees. In the present study, foliar N metabolism of adult trees of three coastal and one interior provenance of Douglas-fir grown at two common gardens in southwestern Germany (Wiesloch, W; Schluchsee, S) were characterized in two subsequent years. Both the native North American habitats of the seed sources and the common garden sites in Germany differ in climate conditions. Total and mineral soil N as well as soil water content were higher in S compared to W. We hypothesized that i) provenances differ constitutively in N pool sizes and composition, ii) N pools are affected by environmental conditions, and iii) that effects of environmental factors on N pools differ among interior and coastal provenances. Soil water content strongly affected the concentrations of total N, soluble protein, total amino acids (TAA), arginine and glutamate. Foliar concentrations of total N, soluble protein, structural N and TAA of trees grown at W were much higher than in trees at S. Provenance effects were small but significant for total N and soluble protein content (interior provenance showed lowest concentrations), as well as arginine, asparagine and glutamate. Our data suggest that needle N status of adult Douglas-fir is independent from soil N availability and that low soil water availability induces a re-allocation of N from structural N to metabolic N pools. Small provenance effects on N pools suggest that local adaptation of Douglas-fir is not dominated by N conditions at the native habitats.
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Affiliation(s)
- Baoguo Du
- College of Life Science and Biotechnology, Mianyang Normal University, Mianyang, China
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Jürgen Kreuzwieser
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Michael Dannenmann
- Karlsruhe Institute of Technology (KIT) Campus Alpin, Institute of Meteorology and Climate Research (IMK), Atmospheric Environmental Research (IMK-IFU), Garmisch-Partenkirchen, Germany
| | - Laura Verena Junker
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, Mississauga, Ontario, Canada
- Forest Research Institute Baden-Württemberg (FVA), Freiburg, Germany
| | - Anita Kleiber
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Moritz Hess
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, Mississauga, Ontario, Canada
- Forest Research Institute Baden-Württemberg (FVA), Freiburg, Germany
- Institute of Medical Biometry, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, Mainz, Germany
| | - Kirstin Jansen
- Institute for Landscape Biogeochemistry, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
- Institute of Ecology, Leuphana University of Lüneburg, Lüneburg, Germany
| | - Monika Eiblmeier
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Arthur Gessler
- Institute for Landscape Biogeochemistry, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Ulrich Kohnle
- Forest Research Institute Baden-Württemberg (FVA), Freiburg, Germany
| | - Ingo Ensminger
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, Mississauga, Ontario, Canada
- Forest Research Institute Baden-Württemberg (FVA), Freiburg, Germany
| | - Heinz Rennenberg
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- King Saud University, Riyadh, Saudi Arabia
| | - Henning Wildhagen
- Forest Research Institute Baden-Württemberg (FVA), Freiburg, Germany
- * E-mail:
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Liu K, Ding X, Tang X, Wang J, Li W, Yan Q, Liu Z. Macro and Microelements Drive Diversity and Composition of Prokaryotic and Fungal Communities in Hypersaline Sediments and Saline-Alkaline Soils. Front Microbiol 2018. [PMID: 29535703 PMCID: PMC5835090 DOI: 10.3389/fmicb.2018.00352] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differed significantly between the sediments and saline soils. The compositions of prokaryotic and fungal communities in the hypersaline sediments were different from those in adjacent saline–alkaline soils, indicating a habitat-specific microbial distribution pattern. The macroelements (S, P, K, Mg, and Fe) and Ca were, respectively, correlated closely with the alpha diversity of prokaryotes and fungi, while the macronutrients (e.g., Na, S, P, and Ca) were correlated with the prokaryotic and fungal beta-diversity (P ≤ 0.05). And, the nine microelements (e.g., Al, Ba, Co, Hg, and Mn) and micronutrients (Ba, Cd, and Sr) individually shaped the alpha diversity of prokaryotes and fungi, while the six microelements (e.g., As, Ba, Cr, and Ge) and only the trace elements (Cr and Cu), respectively, influenced the beta diversity of prokaryotes and fungi (P < 0.05). Variation-partitioning analysis (VPA) showed that environmental variables jointly explained 55.49% and 32.27% of the total variation for the prokaryotic and fungal communities, respectively. Together, our findings demonstrate that the diversity and community composition of the prokaryotes and fungi were driven by different macro and microelements in saline habitats, and that geochemical elements could more widely regulate the diversity and community composition of prokaryotes than these of fungi.
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Affiliation(s)
- Kaihui Liu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Xiaowei Ding
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Xiaofei Tang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Wenjun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiome Research Center and School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
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11
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Maltz MR, Treseder KK, McGuire KL. Links between plant and fungal diversity in habitat fragments of coastal shrubland. PLoS One 2017; 12:e0184991. [PMID: 28926606 PMCID: PMC5604993 DOI: 10.1371/journal.pone.0184991] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/04/2017] [Indexed: 12/03/2022] Open
Abstract
Habitat fragmentation is widespread across ecosystems, detrimentally affecting biodiversity. Although most habitat fragmentation studies have been conducted on macroscopic organisms, microbial communities and fungal processes may also be threatened by fragmentation. This study investigated whether fragmentation, and the effects of fragmentation on plants, altered fungal diversity and function within a fragmented shrubland in southern California. Using fluorimetric techniques, we assayed enzymes from plant litter collected from fragments of varying sizes to investigate enzymatic responses to fragmentation. To isolate the effects of plant richness from those of fragment size on fungi, we deployed litter bags containing different levels of plant litter diversity into the largest fragment and incubated in the field for one year. Following field incubation, we determined litter mass loss and conducted molecular analyses of fungal communities. We found that leaf-litter enzyme activity declined in smaller habitat fragments with less diverse vegetation. Moreover, we detected greater litter mass loss in litter bags containing more diverse plant litter. Additionally, bags with greater plant litter diversity harbored greater numbers of fungal taxa. These findings suggest that both plant litter resources and fungal function may be affected by habitat fragmentation’s constraints on plants, possibly because plant species differ chemically, and may thus decompose at different rates. Diverse plant assemblages may produce a greater variety of litter resources and provide more ecological niche space, which may support greater numbers of fungal taxa. Thus, reduced plant diversity may constrain both fungal taxa richness and decomposition in fragmented coastal shrublands. Altogether, our findings provide evidence that even fungi may be affected by human-driven habitat fragmentation via direct effects of fragmentation on plants. Our findings underscore the importance of restoring diverse vegetation communities within larger coastal sage scrub fragments and suggest that this may be an effective way to improve the functional capacity of degraded sites.
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Affiliation(s)
- Mia R. Maltz
- Center for Conservation Biology, University of California Riverside, Riverside, California, United States of America
- * E-mail:
| | - Kathleen K. Treseder
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
| | - Krista L. McGuire
- Department of Biology, University of Oregon, Eugene, Oregon, United States of America
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12
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Tian J, He N, Hale L, Niu S, Yu G, Liu Y, Blagodatskaya E, Kuzyakov Y, Gao Q, Zhou J. Soil organic matter availability and climate drive latitudinal patterns in bacterial diversity from tropical to cold temperate forests. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12952] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jing Tian
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Nianpeng He
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Lauren Hale
- Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental SciencesInstitute for Environmental GenomicsUniversity of Oklahoma Norman OK USA
| | - Shuli Niu
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Guirui Yu
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Yuan Liu
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Evgenia Blagodatskaya
- Institute of Physicochemical and Biological Problems in Soil Science Pushchino Russia
- Department of Agricultural Soil ScienceUniversity of Göttingen Göttingen Germany
| | - Yakov Kuzyakov
- Department of Agricultural Soil ScienceUniversity of Göttingen Göttingen Germany
- Agro‐Technology InstituteRUDN University Moscow Russia
| | - Qun Gao
- Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental SciencesInstitute for Environmental GenomicsUniversity of Oklahoma Norman OK USA
- State Key Joint Laboratory of Environment Simulation and Pollution ControlSchool of EnvironmentTsinghua University Beijing China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental SciencesInstitute for Environmental GenomicsUniversity of Oklahoma Norman OK USA
- State Key Joint Laboratory of Environment Simulation and Pollution ControlSchool of EnvironmentTsinghua University Beijing China
- Earth and Environmental SciencesLawrence Berkeley National Laboratory Berkeley CA USA
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13
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Nacke H, Goldmann K, Schöning I, Pfeiffer B, Kaiser K, Castillo-Villamizar GA, Schrumpf M, Buscot F, Daniel R, Wubet T. Fine Spatial Scale Variation of Soil Microbial Communities under European Beech and Norway Spruce. Front Microbiol 2016; 7:2067. [PMID: 28066384 PMCID: PMC5177625 DOI: 10.3389/fmicb.2016.02067] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/07/2016] [Indexed: 01/23/2023] Open
Abstract
The complex interactions between trees and soil microbes in forests as well as their inherent seasonal and spatial variations are poorly understood. In this study, we analyzed the effects of major European tree species (Fagus sylvatica L. and Picea abies (L.) Karst) on soil bacterial and fungal communities. Mineral soil samples were collected from different depths (0-10, 10-20 cm) and at different horizontal distances from beech or spruce trunks (0.5, 1.5, 2.5, 3.5 m) in early summer and autumn. We assessed the composition of soil bacterial and fungal communities based on 16S rRNA gene and ITS DNA sequences. Community composition of bacteria and fungi was most strongly affected by soil pH and tree species. Different ectomycorrhizal fungi (e.g., Tylospora) known to establish mutualistic associations with plant roots showed a tree species preference. Moreover, bacterial and fungal community composition showed spatial and seasonal shifts in soil surrounding beech and spruce. The relative abundance of saprotrophic fungi was higher at a depth of 0-10 vs. 10-20 cm depth. This was presumably a result of changes in nutrient availability, as litter input and organic carbon content decreased with soil depth. Overall bacterial community composition showed strong variations under spruce with increasing distance from the tree trunks, which might be attributed in part to higher fine root biomass near spruce trunks. Furthermore, overall bacterial community composition was strongly affected by season under deciduous trees.
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Affiliation(s)
- Heiko Nacke
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August UniversityGöttingen, Germany
| | - Kezia Goldmann
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental ResearchHalle, Germany
- Department of Biology II, University of LeipzigLeipzig, Germany
| | - Ingo Schöning
- Max Planck Institute for BiogeochemistryJena, Germany
| | - Birgit Pfeiffer
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August UniversityGöttingen, Germany
| | - Kristin Kaiser
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August UniversityGöttingen, Germany
| | - Genis A. Castillo-Villamizar
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August UniversityGöttingen, Germany
| | | | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental ResearchHalle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August UniversityGöttingen, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental ResearchHalle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
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14
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Tu Q, Deng Y, Yan Q, Shen L, Lin L, He Z, Wu L, Van Nostrand JD, Buzzard V, Michaletz ST, Enquist BJ, Weiser MD, Kaspari M, Waide RB, Brown JH, Zhou J. Biogeographic patterns of soil diazotrophic communities across six forests in North America. Mol Ecol 2016; 25:2937-48. [PMID: 27085668 DOI: 10.1111/mec.13651] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/23/2016] [Accepted: 04/12/2016] [Indexed: 11/29/2022]
Abstract
Soil diazotrophs play important roles in ecosystem functioning by converting atmospheric N2 into biologically available ammonium. However, the diversity and distribution of soil diazotrophic communities in different forests and whether they follow biogeographic patterns similar to macroorganisms still remain unclear. By sequencing nifH gene amplicons, we surveyed the diversity, structure and biogeographic patterns of soil diazotrophic communities across six North American forests (126 nested samples). Our results showed that each forest harboured markedly different soil diazotrophic communities and that these communities followed traditional biogeographic patterns similar to plant and animal communities, including the taxa-area relationship (TAR) and latitudinal diversity gradient. Significantly higher community diversity and lower microbial spatial turnover rates (i.e. z-values) were found for rainforests (~0.06) than temperate forests (~0.1). The gradient pattern of TARs and community diversity was strongly correlated (r(2) > 0.5) with latitude, annual mean temperature, plant species richness and precipitation, and weakly correlated (r(2) < 0.25) with pH and soil moisture. This study suggests that even microbial subcommunities (e.g. soil diazotrophs) follow general biogeographic patterns (e.g. TAR, latitudinal diversity gradient), and indicates that the metabolic theory of ecology and habitat heterogeneity may be the major underlying ecological mechanisms shaping the biogeographic patterns of soil diazotrophic communities.
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Affiliation(s)
- Qichao Tu
- Department of Marine Sciences, Ocean College, Zhejiang University, Zhejiang, 310058, China.,Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Ye Deng
- Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, 100085, China
| | - Qingyun Yan
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Lina Shen
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Lu Lin
- Department of Marine Sciences, Ocean College, Zhejiang University, Zhejiang, 310058, China
| | - Zhili He
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Liyou Wu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Joy D Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Vanessa Buzzard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Sean T Michaletz
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.,Earth and Environmental Sciences Division, Los Alamos National Laboratory, MS J495, Los Alamos, NM 87545, USA
| | - Brian J Enquist
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.,The Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM, 87501, USA
| | - Michael D Weiser
- Department of Biology, EEB Graduate Program, University of Oklahoma, Norman, OK, 73019, USA
| | - Michael Kaspari
- Department of Biology, EEB Graduate Program, University of Oklahoma, Norman, OK, 73019, USA.,Smithsonian Tropical Research Institute, Balboa, 0843-03092, Republic of Panama
| | - Robert B Waide
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - James H Brown
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.,Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94270, USA
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