Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field

Franklin, Rima B.; Mills, Aaron L.

doi:10.1016/s0168-6496(03)00074-6

Cited by 288 publications

(200 citation statements)

References 48 publications

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“…The abundance and community compositions of the functional genes involved in denitrification can be affected by many factors, such as competition, predation, water content, pH, O 2 , and substrate availability (Ladd et al 1993;Franklin and Mills 2003). Some studies have investigated the responses of denitrifiers to soil environmental changes.…”

Section: Introductionmentioning

confidence: 99%

Response of denitrification genes nirS, nirK, and nosZ to irrigation water quality in a Chinese agricultural soil

Zhou

Zheng

Shen

et al. 2011

Environ Sci Pollut Res

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Purpose Denitrification is an important biochemical process in global nitrogen cycle, with a potent greenhouse gas product N 2 O. Wastewater irrigation can result in the changes of soil properties and microbial communities of agricultural soils. The purpose of this study was to examine how the soil denitrification genes responded to different irrigation regimes. Materials and methods Soil samples were collected from three rural districts of Beijing (China) with three different irrigation regimes: clean groundwater (CW), reclaimed water (RW), and wastewater (WW). The abundance and diversity of three denitrification microbial genes (nirS, nirK, and nosZ) were examined by real-time polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) molecular approaches. Results and discussion The abundance of nirS in the WW treatment was higher than that in the CW treatment, and no significant difference was found between the RW and CW or WW treatments. The abundance of nirK gene of the RW and WW treatments was higher than that of the CW treatment. There was no difference for nosZ gene among the three treatments. Correspondence analysis based on the DGGE profiles showed that there was no obvious difference in the nosZ gene composition, but nirS and nirK genes changed with different irrigation regimes. Conclusions Irrigation with unclean water sources enhanced the soil NO 3 − content and changed the abundance and composition of soil denitrifiers, and different functional genes had different responses. Irrigation with unclean water sources increased the abundance of nirK gene and changed the community structures of nirS and nirK genes, while nosZ gene was relatively stable in the soil. These results could be helpful to explore the mechanisms of the variation of denitrification processes under long-term wastewater irrigation and partially explain the reason of more N 2 O output in the field with wastewater irrigation.

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Section: Introductionmentioning

confidence: 99%

Response of denitrification genes nirS, nirK, and nosZ to irrigation water quality in a Chinese agricultural soil

Zhou

Zheng

Shen

et al. 2011

Environ Sci Pollut Res

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“…To identify local factors that may influence the spatial distribution of diversity, including competitive interactions and resource availability, information on how phenotypes and genotypes are arrayed in space is crucial. There is a growing body of empirical studies examining the spatial distribution of genetic diversity in the soil at a range of spatial scales from micrometers to kilometers [3,8,20,25,48,56,69).…”

Section: Introductionmentioning

confidence: 99%

Spatial Variation in Streptomyces Genetic Composition and Diversity in a Prairie Soil

et al. 2004

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Understanding how microbial genotypes are arrayed in space is crucial for identifying local factors that may influence the spatial distribution of genetic diversity. In this study we investigated variation in 16S rDNA sequences and rep-PCR fingerprints of Streptomyces stains isolated from prairie soil among three locations and four soil depths. Substantial variation in Streptomyces OTU (operational taxonomic unit) and BOX-PCR fingerprint diversity was found among locations within a limited spatial area (1 m 2 ). Further, phylogenetic lineages at each location were distinct. However, there was little variation in genetic diversity among isolates from different soil depths and similar phylogenetic lineages were found at each depth. Some clones were found at a localized scale while other clones had a relatively widespread distribution. There was poor correspondence between 16S rDNA groupings and rep-PCR fingerprint groupings. The finding of distinct phylogenetic lineages and the variation in spatial distribution of clones suggests that selection pressures may vary over the soil landscape.

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“…Soil community structures differ markedly between systems, and even across landscapes that appear macroscopically homogeneous. (for example, Axelrood et al, 2002;Franklin and Mills, 2003;Hackl et al, 2004;Sliwinski and Goodman, 2004;Oline, 2006;Herrera et al, 2007;Lamarche et al, 2007). Whole community studies and studies on the genotypes of individual taxa have revealed that, at high levels of taxonomic resolution, there is a degree of prokaryote endemism apparent across broad geographic scales (Fulthorpe et al, 1998;Cho and Tiedje, 2000;Wawrik et al, 2007).…”

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confidence: 99%

Distantly sampled soils carry few species in common

et al. 2008

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The bacterial phylogenetic structure of soils from four distinctly different sites in South and North America was analyzed. One hundred and thirty-nine thousand sequences of the V9 region of the small subunit of the bacterial ribosomal RNA gene generated for a previous study were used for this work. Whereas the previous work estimated levels of species richness, this study details the degree of bacterial community overlap between the four soils. Sequences from the four soils were classified and grouped into different phyla and then assigned to operational taxonomic units (OTUs) as defined by 97 or 100% sequence similarity. Pairwise Jaccard and h similarity indices averaged over all phyla equalled 6 and 12% respectively at the 97% similarity level, and 15% for both at the 100% similarity level. At 100 and 97% sequence similarity, 1.5 and 4.1% of OTUs were found in all four soils respectively, and 87.9 and 74.4%, respectively were a unique particular soil. These analyses, based on the largest soil bacterial sequence retrieval to date, establish the high degree of community structure difference for randomly sampled dissimilar soils and support the idea that wide sampling is important for bioprospecting. The 10 most abundant cultured genera were determined in each soil. These 10 genera comprised a significant proportion of the reads obtained from each soil (31.3-37.4%). Chitinophaga was the most abundant or the second most abundant genus in all four soils with 7.5-13.8% of the total bacterial sequences in these soils. The striking result is that several culturable genera, whose roles in soil are virtually unknown, were found among these dominant sequences.

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Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field

Cited by 288 publications

References 48 publications

Response of denitrification genes nirS, nirK, and nosZ to irrigation water quality in a Chinese agricultural soil

Response of denitrification genes nirS, nirK, and nosZ to irrigation water quality in a Chinese agricultural soil

Spatial Variation in Streptomyces Genetic Composition and Diversity in a Prairie Soil

Distantly sampled soils carry few species in common

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