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Changes of microbial population and N-cycling function genes with depth in three Chinese paddy soils

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      Abstract

      Microbial communities play critical roles in soil nitrogen (N) cycle; however, we have limited understanding of the distribution of N-cycling microbial groups in deeper soil horizons. In this study, we used quantitative PCR to characterize the changes of microbial populations (16S rRNA and 18S rRNA) and five key N-cycling gene abundances involved in N fixation (nifH), ammonia oxidation (amoA) by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), and nitrite reduction (nirS and nirK) along profiles (0–100 cm depth) of different paddy soils from three regions (Hailun, Changshu, Yingtan) across China from north to south. We found that most microbial and N-cycling functional genes significantly decreased with soil depth; however, AOA were enriched in deeper soil layers (20–40 cm). The abundances of microbial and N-cycling functional genes generally decreased by one to two orders of magnitude in the deeper horizons relative to topsoils. The AOA gene abundance was higher than that of AOB in the paddy soil profile, and the nirS and nirK abundances were dominant in topsoil and deeper soil, respectively. All N functional genes except AOA were more abundant in Changshu than Hailun and Yingtan. High abundances and low vertical changes of N-cycling genes in Changshu suggest more dynamic N-transformations in this region. Correlation analysis showed that soil properties and climate parameters had a significant relationship with N-cycling gene abundances. Moreover, the abundance of different N-cycling genes was affected by different environmental parameters, which should be studied further to explore their roles in N cycling for sustainable agriculture and environmental management.

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      The diversity and biogeography of soil bacterial communities.

      For centuries, biologists have studied patterns of plant and animal diversity at continental scales. Until recently, similar studies were impossible for microorganisms, arguably the most diverse and abundant group of organisms on Earth. Here, we present a continental-scale description of soil bacterial communities and the environmental factors influencing their biodiversity. We collected 98 soil samples from across North and South America and used a ribosomal DNA-fingerprinting method to compare bacterial community composition and diversity quantitatively across sites. Bacterial diversity was unrelated to site temperature, latitude, and other variables that typically predict plant and animal diversity, and community composition was largely independent of geographic distance. The diversity and richness of soil bacterial communities differed by ecosystem type, and these differences could largely be explained by soil pH (r(2) = 0.70 and r(2) = 0.58, respectively; P < 0.0001 in both cases). Bacterial diversity was highest in neutral soils and lower in acidic soils, with soils from the Peruvian Amazon the most acidic and least diverse in our study. Our results suggest that microbial biogeography is controlled primarily by edaphic variables and differs fundamentally from the biogeography of "macro" organisms.
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        Nitrogen Cycles: Past, Present, and Future

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          Archaea predominate among ammonia-oxidizing prokaryotes in soils.

          Ammonia oxidation is the first step in nitrification, a key process in the global nitrogen cycle that results in the formation of nitrate through microbial activity. The increase in nitrate availability in soils is important for plant nutrition, but it also has considerable impact on groundwater pollution owing to leaching. Here we show that archaeal ammonia oxidizers are more abundant in soils than their well-known bacterial counterparts. We investigated the abundance of the gene encoding a subunit of the key enzyme ammonia monooxygenase (amoA) in 12 pristine and agricultural soils of three climatic zones. amoA gene copies of Crenarchaeota (Archaea) were up to 3,000-fold more abundant than bacterial amoA genes. High amounts of crenarchaeota-specific lipids, including crenarchaeol, correlated with the abundance of archaeal amoA gene copies. Furthermore, reverse transcription quantitative PCR studies and complementary DNA analysis using novel cloning-independent pyrosequencing technology demonstrated the activity of the archaea in situ and supported the numerical dominance of archaeal over bacterial ammonia oxidizers. Our results indicate that crenarchaeota may be the most abundant ammonia-oxidizing organisms in soil ecosystems on Earth.
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            Author and article information

            Affiliations
            [1 ] Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
            [2 ] Graduate University of Chinese Academy of Sciences, Beijing, China
            The University of Akron, UNITED STATES
            Author notes

            Competing Interests: The authors have declared that no competing interests exist.

            Contributors
            Role: Conceptualization, Role: Data curation, Role: Formal analysis, Role: Methodology, Role: Validation, Role: Writing – original draft, Role: Writing – review & editing
            Role: Data curation, Role: Methodology, Role: Software
            Role: Data curation, Role: Methodology
            ORCID: http://orcid.org/0000-0002-6585-2330, Role: Conceptualization, Role: Formal analysis, Role: Funding acquisition, Role: Resources, Role: Supervision, Role: Validation, Role: Writing – original draft, Role: Writing – review & editing
            Role: Data curation, Role: Methodology, Role: Software
            Role: Conceptualization, Role: Investigation, Role: Visualization, Role: Writing – review & editing
            Role: Editor
            Journal
            PLoS One
            PLoS ONE
            plos
            plosone
            PLoS ONE
            Public Library of Science (San Francisco, CA USA )
            1932-6203
            28 December 2017
            2017
            : 12
            : 12
            29284018
            5746221
            10.1371/journal.pone.0189506
            PONE-D-17-31840
            (Editor)
            © 2017 Wang et al

            This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

            Counts
            Figures: 6, Tables: 3, Pages: 16
            Product
            Funding
            Funded by: The Strategic Priority Research Program of the Chinese Academy of Sciences
            Award ID: XDB15010101
            Award Recipient : ORCID: http://orcid.org/0000-0002-6585-2330
            This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB15010101). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
            Categories
            Research Article
            Biology and life sciences
            Biochemistry
            Nucleic acids
            RNA
            Non-coding RNA
            Ribosomal RNA
            Biology and life sciences
            Biochemistry
            Ribosomes
            Ribosomal RNA
            Biology and life sciences
            Cell biology
            Cellular structures and organelles
            Ribosomes
            Ribosomal RNA
            Biology and Life Sciences
            Genetics
            Fungal Genetics
            Biology and Life Sciences
            Mycology
            Fungal Genetics
            Biology and Life Sciences
            Organisms
            Bacteria
            Biology and Life Sciences
            Organisms
            Eukaryota
            Plants
            Grasses
            Rice
            Research and Analysis Methods
            Experimental Organism Systems
            Plant and Algal Models
            Rice
            Biology and Life Sciences
            Organisms
            Eukaryota
            Fungi
            Biology and Life Sciences
            Mycology
            Fungal Structure
            Biology and Life Sciences
            Agriculture
            Agricultural Soil Science
            Ecology and Environmental Sciences
            Soil Science
            Agricultural Soil Science
            Physical Sciences
            Chemistry
            Chemical Compounds
            Ammonia
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            All relevant data are within the paper.

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