Biogeographic Distribution Patterns of the Archaeal Communities Across the Black Soil Zone of Northeast China
Although archaea are ubiquitous in various environments, the knowledge gaps still exist regarding the biogeographical distribution of archaeal communities at regional scales in agricultural soils compared with bacteria and fungi. To provide a broader biogeographical context of archaeal diversity, th...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-01-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2019.00023/full |
| _version_ | 1818136245822291968 |
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| author | Junjie Liu Zhenhua Yu Qin Yao Yueyu Sui Yu Shi Haiyan Chu Caixian Tang Ashley E. Franks Ashley E. Franks Jian Jin Xiaobing Liu Guanghua Wang |
| author_facet | Junjie Liu Zhenhua Yu Qin Yao Yueyu Sui Yu Shi Haiyan Chu Caixian Tang Ashley E. Franks Ashley E. Franks Jian Jin Xiaobing Liu Guanghua Wang |
| author_sort | Junjie Liu |
| collection | DOAJ |
| description | Although archaea are ubiquitous in various environments, the knowledge gaps still exist regarding the biogeographical distribution of archaeal communities at regional scales in agricultural soils compared with bacteria and fungi. To provide a broader biogeographical context of archaeal diversity, this study quantified the abundance and community composition of archaea across the black soil zone in northeast China using real-time PCR and high-throughput sequencing (HTS) methods. Archaeal abundances across all soil samples ranged from 4.04 × 107 to 26.18 × 107 16S rRNA gene copies per gram of dry soil. Several soil factors were positively correlated with the abundances including soil pH, concentrations of total C, N, and P, and available K in soil, and soil water content. Approximately 94.2, 5.7, and 0.3% of archaeal sequences, and 31, 151, and 3 OTUs aligned within the phyla Thaumarchaeota, Euryarchaeota, and Crenarchaeota, respectively. Within the phylum of Thaumarchaeota, group 1.1b was a dominating genus accounting for an average of 87% archaeal sequences and phylogenetically classified as Nitrososphaera, a genus of ammonia oxidizing archaea. The response of dominating OTUs to environmental factors differed greatly, suggesting the physiological characteristics of different archaeal members is diversified in the black soils. Although the number of OTUs was not related with any particular soil parameters, the number of OTUs within Thaumarchaeota and Euryarchaeota was marginally related with soil pH. Archaeal community compositions differed between samples, and a Canonical correspondence analysis (CCA) analysis indicated that soil pH and the latitude of sampling locations were two dominating factors in shifting community structures. A variance partitioning analysis (VPA) analysis showed that the selected soil parameters (32%) were the largest drivers of community variation, in particular soil pH (21%), followed by geographic distances (19%). These findings suggest that archaeal communities have distinct biogeographic distribution pattern in the black soil zone and soil pH was the key edaphic factor in structuring the community compositions. |
| first_indexed | 2024-12-11T09:37:21Z |
| format | Article |
| id | doaj.art-4b25b22db4444561b3039de0c1583d6d |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-11T09:37:21Z |
| publishDate | 2019-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-4b25b22db4444561b3039de0c1583d6d2022-12-22T01:12:49ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2019-01-011010.3389/fmicb.2019.00023423094Biogeographic Distribution Patterns of the Archaeal Communities Across the Black Soil Zone of Northeast ChinaJunjie Liu0Zhenhua Yu1Qin Yao2Yueyu Sui3Yu Shi4Haiyan Chu5Caixian Tang6Ashley E. Franks7Ashley E. Franks8Jian Jin9Xiaobing Liu10Guanghua Wang11Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, ChinaKey Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, ChinaKey Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, ChinaKey Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, ChinaState Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, ChinaState Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, ChinaDepartment of Animal, Plant and Soil Sciences, AgriBio Centre for AgriBiosciences, La Trobe University, Bundoora, VIC, AustraliaDepartment of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC, AustraliaResearch Centre for Future Landscapes, La Trobe University, Melbourne, VIC, AustraliaKey Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, ChinaKey Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, ChinaKey Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, ChinaAlthough archaea are ubiquitous in various environments, the knowledge gaps still exist regarding the biogeographical distribution of archaeal communities at regional scales in agricultural soils compared with bacteria and fungi. To provide a broader biogeographical context of archaeal diversity, this study quantified the abundance and community composition of archaea across the black soil zone in northeast China using real-time PCR and high-throughput sequencing (HTS) methods. Archaeal abundances across all soil samples ranged from 4.04 × 107 to 26.18 × 107 16S rRNA gene copies per gram of dry soil. Several soil factors were positively correlated with the abundances including soil pH, concentrations of total C, N, and P, and available K in soil, and soil water content. Approximately 94.2, 5.7, and 0.3% of archaeal sequences, and 31, 151, and 3 OTUs aligned within the phyla Thaumarchaeota, Euryarchaeota, and Crenarchaeota, respectively. Within the phylum of Thaumarchaeota, group 1.1b was a dominating genus accounting for an average of 87% archaeal sequences and phylogenetically classified as Nitrososphaera, a genus of ammonia oxidizing archaea. The response of dominating OTUs to environmental factors differed greatly, suggesting the physiological characteristics of different archaeal members is diversified in the black soils. Although the number of OTUs was not related with any particular soil parameters, the number of OTUs within Thaumarchaeota and Euryarchaeota was marginally related with soil pH. Archaeal community compositions differed between samples, and a Canonical correspondence analysis (CCA) analysis indicated that soil pH and the latitude of sampling locations were two dominating factors in shifting community structures. A variance partitioning analysis (VPA) analysis showed that the selected soil parameters (32%) were the largest drivers of community variation, in particular soil pH (21%), followed by geographic distances (19%). These findings suggest that archaeal communities have distinct biogeographic distribution pattern in the black soil zone and soil pH was the key edaphic factor in structuring the community compositions.https://www.frontiersin.org/article/10.3389/fmicb.2019.00023/full16S rRNA geneIllumina MiSeq sequencingMollisolsreal-time PCRThaumarchaeota |
| spellingShingle | Junjie Liu Zhenhua Yu Qin Yao Yueyu Sui Yu Shi Haiyan Chu Caixian Tang Ashley E. Franks Ashley E. Franks Jian Jin Xiaobing Liu Guanghua Wang Biogeographic Distribution Patterns of the Archaeal Communities Across the Black Soil Zone of Northeast China Frontiers in Microbiology 16S rRNA gene Illumina MiSeq sequencing Mollisols real-time PCR Thaumarchaeota |
| title | Biogeographic Distribution Patterns of the Archaeal Communities Across the Black Soil Zone of Northeast China |
| title_full | Biogeographic Distribution Patterns of the Archaeal Communities Across the Black Soil Zone of Northeast China |
| title_fullStr | Biogeographic Distribution Patterns of the Archaeal Communities Across the Black Soil Zone of Northeast China |
| title_full_unstemmed | Biogeographic Distribution Patterns of the Archaeal Communities Across the Black Soil Zone of Northeast China |
| title_short | Biogeographic Distribution Patterns of the Archaeal Communities Across the Black Soil Zone of Northeast China |
| title_sort | biogeographic distribution patterns of the archaeal communities across the black soil zone of northeast china |
| topic | 16S rRNA gene Illumina MiSeq sequencing Mollisols real-time PCR Thaumarchaeota |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2019.00023/full |
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